CHANGES IN R 3.0.1| NEWS | R Documentation |
CHANGES IN R 3.0.1chooseCRANmirror() and chooseBioCmirror() gain
an ind argument (like setRepositories()).
mcparallel has a new argument mc.interactive
which can modify the interactive flag in the child process. The
new default is FALSE which makes child processes
non-interactive by default (this prevents lock-ups due to children
waiting for interactive input).
scan() now warns when end-of-file occurs within
a quoted string.
count.fields() is now consistent with scan()
in its handling of newlines in quoted strings. Instead of
triggering an error, this results in the current line receiving
NA as the field count, with the next line getting the total
count of the two lines.
The default method of image() will plot axes of the
class of xlim and ylim (and hence of x and
y if there is a suitable range() method). Based on
a suggestion of Michael Sumner.
load() now has a verbose argument for
debugging support, to print the names of objects just before
loading them.
When loading a serialized object encounters a reference to a namespace which cannot be loaded, this is replaced by a reference to the global environment, with a warning.
pairs() gains a line.main option for title placement.
The remaining instances in which serialization to a raw vector was limited to 2GB have been unlimited on a 64-bit platform, and in most cases serialization to a vector of more than 1GB will be substantially faster.
R CMD config now make use of personal
‘Makevars’ files under ‘~/.R’ and a site file
‘Makevars.site’, in the same way as R CMD SHLIB and
R CMD INSTALL. This makes the utility more useful in
package configure scripts.
On Windows finding the personal files may require the environment variable HOME set.
The old behaviour can be obtained with the new options --no-user-files and --no-site-files.
Alternatives to the site and user customization files ‘Makevars.site’ and ‘~/.R/Makevars’ can be specified via the environment variables R_MAKEVARS_SITE and R_MAKEVARS_USER respectively. These can be used to suppress the use of the default files by setting an empty value (where possible) or a non-existent path.
sys.source() did not report error locations when
keep.source = TRUE.
as.POSIXct.numeric was coercing origin using
the tz argument and not "GMT" as documented
(PR#14973).
The active binding to assign fields in reference classes has been cleaned up to reduce dependence on the class' package environment, also fixing bug in initializing read-only fields (inspired by a report from Hadley Wickham).
str(d) no longer gives an error when names(d)
contain illegal multibyte strings (PR#15247).
Profiling of built-in functions with line.profiling=
TRUE did not record the line from which they were called.
citation(pkg) dropped the header and footer specified
in the ‘CITATION’ file (PR#15257).
Quotes were handled differently when reading the first line
and reading the rest, so read.table() misread some files
that contained quote characters (PR#15245).
cat() with sep a character vector of length
greater than one and more than one argument was using separators
inconsistently (PR#15261).
On Windows in R 3.0.0, savePlot() failed because of
an incorrect check on the argument count.
unzip(list = TRUE) returned Names as a factor
and not a character vector (as documented) for the internal method.
(Noticed by Sean O'Riordain.)
contourLines() now checks more comprehensively for
conformance of its x, y and z arguments (it
was used incorrectly in package R2G2).
Saved graphics display lists are R version-specific. Attempting to load workspaces containing them (or some other version-specific objects) aborted the load in R 3.0.0 and earlier; now it does a partial load and generates a warning instead.
In R 3.0.0, identify() and locator() did
not record information correctly, so replaying a graph (e.g. by
copying it to another device) would fail. (PR#15271)
Calling file.copy() or dirname() with the
invalid input "" (which was being used in packages, despite
not being a file path) could have caused a segfault.
dirname("") is now "" rather than "." (unless
it segfaulted).
supsmu() could read/write outside its input vectors
for very short inputs (seen in package rms for n = 4).
as.dendrogram()'s hclust method uses less
memory and hence gets considerably faster for large (n ~ 1000)
clusterings, thanks to Daniel Müllner. (PR#15174)
The return value when all workers failed from
parallel::mclapply(mc.presechedule = TRUE) was a list of
strings and not of error objects. (Spotted by Karl Forner and
Bernd Bischl.)
In R 3.0.0, when help() found multiple pages with
the same alias, the HTML display of all the selections was not
produced. (PR#15282)
splinefun(method="monoH.FC") now produces a
function with first argument named x and allows
deriv=3, as documented. (PR#15273)
summaryRprof() would only read the first
chunksize lines of an Rprof file produced with
line.profiling=TRUE. By default, this is the first 100
seconds. (PR#15288)
lsfit() produced an incorrect error message when
argument x had more columns than rows or x had a
different number of rows than y. (Spotted by Renaud Gaujoux.)
Binary operations on equal length vectors copied the class name from the second operand when the first had no class name, but did not set the object bit. (PR#15299)
The trace() method for reference generator objects
failed after those objects became function definitions.
write.table() did not check that factors were
constructed correctly, and so caused a segment fault when
writing bad ones. (PR#15300)
The internal HTTP server no longer chokes on POST requests without body. It will also pass-through other request types for custom handlers (with the method stored in Request-Method header) instead of failing.
CHANGES IN R 3.0.0Packages need to be (re-)installed under this version (3.0.0) of R.
There is a subtle change in behaviour for numeric index
values 2^31 and larger. These never used to be
legitimate and so were treated as NA, sometimes with a
warning. They are now legal for long vectors so there is no
longer a warning, and x[2^31] <- y will now extend the
vector on a 64-bit platform and give an error on a 32-bit one.
It is now possible for 64-bit builds to allocate amounts of
memory limited only by the OS. It may be wise to use OS
facilities (e.g. ulimit in a bash shell,
limit in csh), to set limits on overall memory
consumption of an R process, particularly in a multi-user
environment. A number of packages need a limit of at least 4GB of
virtual memory to load.
64-bit Windows builds of R are by default limited in memory usage to the amount of RAM installed: this limit can be changed by command-line option --max-mem-size or setting environment variable R_MAX_MEM_SIZE.
Negative numbers for colours are consistently an error: previously they were sometimes taken as transparent, sometimes mapped into the current palette and sometimes an error.
identical() has a new argument,
ignore.environment, used when comparing functions (with
default FALSE as before).
There is a new option, options(CBoundsCheck=), which
controls how .C() and .Fortran() pass arguments to
compiled code. If true (which can be enabled by setting the
environment variable R_C_BOUNDS_CHECK to yes), raw,
integer, double and complex arguments are always copied, and
checked for writing off either end of the array on return from the
compiled code (when a second copy is made). This also checks
individual elements of character vectors passed to .C().
This is not intended for routine use, but can be very helpful in finding segfaults in package code.
In layout(), the limits on the grid size have been
raised (again).
New simple provideDimnames() utility function.
Where methods for length() return a double value
which is representable as an integer (as often happens for package
Matrix), this is converted to an integer.
Matrix indexing of dataframes by two-column numeric indices is now supported for replacement as well as extraction.
setNames() now has a default for its object
argument, useful for a character result.
StructTS() has a revised additive constant in the
loglik component of the result: the previous definition is
returned as the loglik0 component. However, the help page has
always warned of a lack of comparability of log-likelihoods for
non-stationary models. (Suggested by Jouni Helske.)
The logic in aggregate.formula() has been revised.
It is now possible to use a formula stored in a variable;
previously, it had to be given explicitly in the function call.
install.packages() has a new argument quiet to
reduce the amount of output shown.
Setting an element of the graphics argument lwd to a
negative or infinite value is now an error. Lines corresponding
to elements with values NA or NaN are silently
omitted.
Previously the behaviour was device-dependent.
Setting graphical parameters cex, col,
lty, lwd and pch in par() now requires a
length-one argument. Previously some silently took the first
element of a longer vector, but not always when documented to do so.
Sys.which() when used with inputs which would be
unsafe in a shell (e.g. absolute paths containing spaces) now uses
appropriate quoting.
as.tclObj() has been extended to handle raw vectors.
Previously, it only worked in the other direction.
(Contributed by Charlie Friedemann, PR#14939.)
New functions cite() and citeNatbib() have
been added, to allow generation of in-text citations from
"bibentry" objects. A cite() function may be added
to bibstyle() environments.
A sort() method has been added for "bibentry"
objects.
The bibstyle() function now defaults to setting the
default bibliography style. The getBibstyle() function
has been added to report the name of the current default style.
scatter.smooth() now has an argument lpars to
pass arguments to lines().
pairs() has a new log argument, to allow some
or all variables to be plotted on logarithmic scale.
(In part, wish of PR#14919.)
split() gains a sep argument.
termplot() does a better job when given a model with
interactions (and no longer attempts to plot interaction terms).
The parser now incorporates code from Romain Francois'
parser package, to support more detailed computation on
the code, such as syntax highlighting, comment-based
documentation, etc. Functions getParseData() and
getParseText() access the data.
There is a new function rep_len() analogous to
rep.int() for when speed is required (and names are not).
The undocumented use rep(NULL, length.out = n) for
n > 0 (which returns NULL) now gives a warning.
demo() gains an encoding argument for those
packages with non-ASCII demos: it defaults to the package encoding
where there is one.
strwrap() converts inputs with a marked encoding to
the current locale: previously it made some attempt to pass
through as bytes inputs invalid in the current locale.
Specifying both rate and scale to
[dpqr]gamma is a warning (if they are essentially the same
value) or an error.
merge() works in more cases where the data frames
include matrices. (Wish of PR#14974.)
optimize() and uniroot() no longer use a
shared parameter object across calls. (nlm(),
nlminb() and optim() with numerical derivatives
still do, as documented.)
The all.equal() method for date-times is now
documented: times are regarded as equal (by default) if they
differ by up to 1 msec.
duplicated() and unique() gain a nmax
argument which can be used to make them much more efficient when
it is known that there are only a small number of unique entries.
This is done automatically for factors.
Functions rbinom(), rgeom(), rhyper(),
rpois(), rnbinom(), rsignrank() and
rwilcox() now return integer (not double) vectors. This
halves the storage requirements for large simulations.
sort(), sort.int() and sort.list() now
use radix sorting for factors of less than 100,000 levels when
method is not supplied. So does order() if called
with a single factor, unless na.last = NA.
diag() as used to generate a diagonal matrix has been
re-written in C for speed and less memory usage. It now forces
the result to be numeric in the case diag(x) since it is
said to have ‘zero off-diagonal entries’.
backsolve() (and forwardsolve()) are now
internal functions, for speed and support for large matrices.
More matrix algebra functions (e.g. chol() and
solve()) accept logical matrices (and coerce to numeric).
sample.int() has some support for n >= 2^31: see its help for the limitations.
A different algorithm is used for (n, size, replace = FALSE,
prob = NULL) for n > 1e7 and size <= n/2. This
is much faster and uses less memory, but does give different results.
approxfun() and splinefun() now return a
wrapper to an internal function in the stats namespace
rather than a .C() or .Call() call. This is more
likely to work if the function is saved and used in a different
session.
The functions .C(), .Call(),
.External() and .Fortran() now give an error (rather
than a warning) if called with a named first argument.
Sweave() by default now reports the locations in
the source file(s) of each chunk.
clearPushBack() is now a documented interface to a
long-existing internal call.
aspell() gains filters for R code, Debian Control
Format and message catalog files, and support for R level
dictionaries. In addition, package utils now provides
functions aspell_package_R_files() and
aspell_package_C_files() for spell checking R and C level
message strings in packages.
bibentry() gains some support for “incomplete”
entries with a crossref field.
gray() and gray.colors() finally allow
alpha to be specified.
monthplot() gains parameters to control the look of
the reference lines. (Suggestion of Ian McLeod.)
Added support for new %~% relation
(“is distributed as”) in plotmath.
domain = NA is accepted by gettext() and
ngettext(), analogously to stop() etc.
termplot() gains a new argument plot = FALSE
which returns information to allow the plots to be modified for
use as part of other plots, but does not plot them.
(Contributed by Terry Therneau, PR#15076.)
quartz.save(), formerly an undocumented part of
R.app, is now available to copy a device to a
quartz() device. dev.copy2pdf() optionally does
this for PDF output: quartz.save() defaults to PNG.
The default method of pairs() now allows
text.panel = NULL and the use of <foo>.panel = NULL
is now documented.
setRefClass() and getRefClass() now return
class generator functions, similar to setClass(), but
still with the reference fields and methods as before
(suggestion of Romain Francois).
New functions bitwNot(), bitwAnd(),
bitwOr() and bitwXor(), using the internal
interfaces previously used for classes "octmode" and
"hexmode".
Also bitwShiftL() and bitwShiftR() for shifting bits
in elements of integer vectors.
New option "deparse.cutoff" to control the deparsing
of language objects such as calls and formulae when printing.
(Suggested by a comment of Sarah Goslee.)
colors() gains an argument distinct.
New demo(colors) and demo(hclColors), with
utility functions.
list.files() (aka dir()) gains a new optional
argument no.. which allows to exclude "." and
".." from listings.
Multiple time series are also of class "matrix";
consequently, head(), e.g., is more useful.
encodeString() preserves UTF-8 marked encodings.
Thus if factor levels are marked as UTF-8 an attempt is made to
print them in UTF-8 in RGui on Windows.
readLines() and scan() (and hence
read.table()) in a UTF-8 locale now discard a UTF-8
byte-order-mark (BOM). Such BOMs are allowed but not recommended
by the Unicode Standard: however Microsoft applications can
produce them and so they are sometimes found on websites.
The encoding name "UTF-8-BOM" for a connection will
ensure that a UTF-8 BOM is discarded.
mapply(FUN, a1, ..) now also works when a1 (or
a further such argument) needs a length() method (which the
documented arguments never do). (Requested by Hervé Pagès; with a
patch.)
.onDetach() is supported as an alternative to
.Last.lib. Unlike .Last.lib, this does not need to
be exported from the package's namespace.
The srcfile argument to parse() may now be a
character string, to be used in error messages.
The format() method for ftable objects gains
a method argument, propagated to write.ftable() and
print(), allowing more compact output, notably for LaTeX
formatting, thanks to Marius Hofert.
The utils::process.events() function has been added
to trigger immediate event handling.
Sys.which() now returns NA (not "") for
NA inputs (related to PR#15147).
The print() method for class "htest" gives
fewer trailing spaces (wish of PR#15124).
Also print output from HoltWinters(), nls() and others.
loadNamespace() allows a version specification to be
given, and this is used to check version specifications given in
the Imports field when a namespace is loaded.
setClass() has a new argument, slots, clearer
and less ambiguous than representation. It is recommended
for future code, but should be back-compatible. At the same time,
the allowed slot specification is slightly more general. See the
documentation for details.
mget() now has a default for envir (the frame
from which it is called), for consistency with get() and
assign().
close() now returns an integer status where available,
invisibly. (Wish of PR#15088.)
The internal method of tar() can now store paths too
long for the ustar format, using the (widely supported) GNU
extension. It can also store long link names, but these are much
less widely supported. There is support for larger files, up to
the ustar limit of 8GB.
Local reference classes have been added to package
methods. These are a technique for avoiding unneeded
copying of large components of objects while retaining standard R
functional behavior. See ?LocalReferenceClasses.
untar() has a new argument restore_times which
if false (not the default) discards the times in the tarball.
This is useful if they are incorrect (some tarballs submitted to
CRAN have times in a local timezone or many years in the
past even though the standard required them to be in UTC).
replayplot() cannot (and will not attempt to) replay
plots recorded under R < 3.0.0. It may crash the R session if
an attempt is made to replay plots created in a different build of
R >= 3.0.0.
Palette changes get recorded on the display list, so
replaying plots (including when resizing screen devices and using
dev.copy()) will work better when the palette is changed
during a plot.
chol(pivot = TRUE) now defaults to LAPACK, not LINPACK.
The parse() function has a new parameter
keep.source, which defaults to options("keep.source").
Profiling via Rprof() now optionally records information
at the statement level, not just the function level.
The Rprof() function now quotes function names in
in its output file on Windows, to be consistent with the quoting
in Unix.
Profiling via Rprof() now optionally records
information about time spent in GC.
The HTML help page for a package now displays non-vignette documentation files in a more accessible format.
To support options(stringsAsFactors = FALSE),
model.frame(), model.matrix() and
replications() now automatically convert character
vectors to factors without a warning.
The print method for objects of class "table"
now detects tables with 0-extents and prints the results as, e.g.,
< table of extent 0 x 1 x 2 >. (Wish of PR#15198.)
Deparsing involving calls to anonymous functions and has been made closer to reversible by the addition of extra parentheses.
The function utils::packageName() has been added as
a lightweight version of methods::getPackageName().
find.package(lib.loc = NULL) now treats loaded
namespaces preferentially in the same way as attached packages
have been for a long time.
In Windows, the Change Directory dialog now defaults to the current working directory, rather than to the last directory chosen in that dialog.
available.packages() gains a
"license/restricts_use" filter which retains only packages
for which installation can proceed solely based on packages which
are guaranteed not to restrict use.
New check_packages_in_dir() function in package
tools for conveniently checking source packages along with
their reverse dependencies.
R's completion mechanism has been improved to handle help requests (starting with a question mark). In particular, help prefixes are now supported, as well as quoted help topics. To support this, completion inside quotes are now handled by R by default on all platforms.
The memory manager now allows the strategy used to balance
garbage collection and memory growth to be controlled by setting
the environment variable R_GC_MEM_GROW. See ?Memory
for more details.
(‘For experts only’, as the introductory manual
says.) The use of environment variables R_NSIZE and
R_VSIZE to control the initial (= minimum) garbage
collection trigger for number of cons cels and size of heap has
been restored: they can be overridden by the command-line options
--min-nsize and --min-vsize; see ?Memory.
On Windows, the device name for bitmap devices as reported
by .Device and .Devices no longer includes the file
name. This is for consistency with other platforms and was
requested by the lattice maintainer.
win.metafile() still uses the file name: the exact form is
used by package tkrplot.
set.seed(NULL) re-initializes .Random.seed as
done at the beginning of the session if not already set.
(Suggestion of Bill Dunlap.)
The breaks argument in hist.default() can now be
a function that returns the breakpoints to be used (previously it
could only return the suggested number of breakpoints).
File ‘share/licenses/licenses.db’ has some clarifications, especially as to which variants of ‘BSD’ and ‘MIT’ is intended and how to apply them to packages. The problematic licence ‘Artistic-1.0’ has been removed.
This section applies only to 64-bit platforms.
There is support for vectors longer than 2^31 - 1 elements. This applies to raw, logical, integer, double, complex and character vectors, as well as lists. (Elements of character vectors remain limited to 2^31 - 1 bytes.)
Most operations which can sensibly be done with long vectors
work: others may return the error ‘long vectors not
supported yet’. Most of these are because they explicitly work
with integer indices (e.g. anyDuplicated() and
match()) or because other limits (e.g. of character strings
or matrix dimensions) would be exceeded or the operations would be
extremely slow.
length() returns a double for long vectors, and
lengths can be set to 2^31 or more by the
replacement function with a double value.
Most aspects of indexing are available. Generally double-valued indices can be used to access elements beyond 2^31 - 1.
There is some support for matrices and arrays with each
dimension less than 2^31 but total number of
elements more than that. Only some aspects of matrix algebra work
for such matrices, often taking a very long time. In other cases
the underlying Fortran code has an unstated restriction (as was
found for complex svd()).
dist() can produce dissimilarity objects for more
than 65536 rows (but for example hclust() cannot process
such objects).
serialize() to a raw vector is unlimited in size
(except by resources).
The C-level function R_alloc can now allocate
2^35 or more bytes.
agrep() and grep() will return double vectors
of indices for long vector inputs.
Many calls to .C() have been replaced by
.Call() to allow long vectors to be supported (now or in
the future). Regrettably several packages had copied the non-API
.C() calls and so failed.
.C() and .Fortran() do not accept long vector
inputs. This is a precaution as it is very unlikely that existing
code will have been written to handle long vectors (and the R
wrappers often assume that length(x) is an integer).
Most of the methods for sort() work for long vectors.
rank(), sort.list() and order() support
long vectors (slowly except for radix sorting).
sample() can do uniform sampling from a long vector.
More use has been made of R objects representing registered entry points, which is more efficient as the address is provided by the loader once only when the package is loaded.
This has been done for packages base, methods,
splines and tcltk: it was already in place for the
other standard packages.
Since these entry points are always accessed by the R entry
points they do not need to be in the load table which can be
substantially smaller and hence searched faster. This does mean
that .C / .Fortran / .Call calls copied from
earlier versions of R may no longer work – but they were never
part of the API.
Many .Call() calls in package base have been
migrated to .Internal() calls.
solve() makes fewer copies, especially when b
is a vector rather than a matrix.
eigen() makes fewer copies if the input has dimnames.
Most of the linear algebra functions make fewer copies when the input(s) are not double (e.g. integer or logical).
A foreign function call (.C() etc) in a package
without a PACKAGE argument will only look in the first DLL
specified in the ‘NAMESPACE’ file of the package rather than
searching all loaded DLLs. A few packages needed PACKAGE
arguments added.
The @<- operator is now implemented as a primitive,
which should reduce some copying of objects when used. Note that
the operator object must now be in package base: do not try
to import it explicitly from package methods.
The transitional support for installing packages without
namespaces (required since R 2.14.0) has been removed.
R CMD build will still add a namespace, but a
.First.lib() function will need to be converted.
R CMD INSTALL no longer adds a namespace (so
installation will fail), and a .First.lib() function in a
package will be ignored (with an installation warning for now).
As an exception, packages without a ‘R’ directory and no ‘NAMESPACE’ file can still be installed.
Packages can specify in their ‘DESCRIPTION file’ a line like
Biarch: yesto be installed on Windows with --force-biarch.
Package vignettes can now be processed by other engines
besides Sweave; see ‘Writing R Extensions’ and the
tools::vignetteEngine help topic for details.
The ‘*.R’ tangled source code for vignettes is now
included in tarballs when R CMD build is used to produce
them. In R 3.0.0, ‘*.R’ files not in the sources will be
produced at install time, but eventually this will be dropped.
The package type "mac.binary" now looks in a path in
the repository without any Mac subtype (which used to be
universal or leopard): it looks in
‘bin/macosx/contrib/3.0’ rather than
‘bin/macosx/leopard/contrib/2.15’). This is the type used
for the CRAN binary distribution for OS X as from R
3.0.0.
File ‘etc/Makeconf’ makes more use of the macros
$(CC), $(CXX), $(F77) and $(FC), so
the compiler in use can be changed by setting just these (and if
necessary the corresponding flags and FLIBS) in file
‘~/.R/Makevars’.
This is convenient for those working with binary distributions of R, e.g. on OS X.
R CMD check now gives a warning rather than a
note if it finds calls to abort, assert or
exit in compiled code, and has been able to find the
‘.o’ file in which the calls occur.
Such calls can terminate the R process which loads the package.
The location of the build and check environment files can now be specified by the environment variables R_BUILD_ENVIRON and R_CHECK_ENVIRON, respectively.
R CMD Sweave gains a --compact option
to control possibly reducing the size of the PDF file it creates
when --pdf is given.
R CMD build now omits Eclipse's ‘.metadata’
directories, and R CMD check warns if it finds them.
R CMD check now does some checks on functions
defined within reference classes, including of .Call() etc
calls.
R CMD check --as-cran notes assignments to the
global environment, calls to data() which load into the
global environment, and calls to attach().
R CMD build by default uses the internal method of
tar() to prepare the tarball. This is more likely to
produce a tarball compatible with R CMD INSTALL and
R CMD check: an external tar program,
including options, can be specified via the environment
variable R_BUILD_TAR.
tools::massageExamples() is better protected against
packages which re-define base functions such as cat() and
get() and so can cause R CMD check to fail when
checking examples.
R CMD javareconf has been enhanced to be more
similar to the code used by configure.
There is now a test that a JNI program can be compiled (like
configure did) and only working settings are used.
It makes use of custom settings from configuration recorded in ‘etc/javaconf’.
The --no-vignettes argument of R CMD
build has been renamed to the more accurate
--no-build-vignettes: its action has always been to
(re)build vignettes and never omitted them.
R CMD check accepts --no-build-vignettes as a
preferred synonym for --no-rebuild-vignettes.
The ENCODING argument to .C() is defunct.
Use iconv() instead.
The .Internal(eval.with.vis) non-API function has
been removed.
Support for the converters for use with .C() has been
removed, including the oft misused non-API header
‘R_ext/RConverters.h’.
The previously deprecated uses of array() with a
0-length dim argument and tapply() with a 0-length
INDEX list are now errors.
Translation packages are defunct.
Calling rep() or rep.int() on a pairlist or
other non-vector object is now an error.
Several non-API entry points have been transferred to
packages (e.g. R_zeroin2) or replaced by different non-API
entry points (e.g. R_tabulate).
The ‘internal’ graphics device invoked by
.Call("R_GD_nullDevice", package = "grDevices") has
been removed: use pdf(file = NULL) instead.
The .Fortran() entry point "dqrls" which has
not been used by R since version 2.15.1 is no longer available.
Functions traceOn() and traceOff() in package
methods are now defunct.
Function CRAN.packages() is finally defunct.
Use of col2rgb(0) is defunct: use par("bg") or
NA instead.
The long-defunct functions Rd_parse(),
anovalist.lm(), categpry(), clearNames(),
gammaCody(), glm.fit.null(), lm.fit.null(),
lm.wfit.null(), manglePackageNames(),
mauchley.test(), package.contents(),
print.coefmat(), reshapeLong(),
reshapeWide(), tkclose(), tkcmd(),
tkfile.dir(), tkfile.tail(), tkopen(),
tkputs(), tkread(), trySilent() and
zip.file.extract() have been removed entirely (but are
still documented in the help system).
The unused dataPath argument to
attachNamespace() has been removed.
grid.prompt() has been removed: use
devAskNewPage() instead.
The long-deprecated intensities component is no
longer returned by hist().
mean() for data frames and sd() for data
frames and matrices are defunct.
chol(pivot = FALSE, LINPACK = TRUE),
ch2inv(LINPACK = TRUE), eigen(EISPACK = TRUE),
solve(LINPACK = TRUE) and svd(LINPACK = TRUE) are
defunct: LAPACK will be used, with a warning.
The keep.source argument to library() and
require() is defunct. This option needs to be set
at install time.
Documentation for real(), as.real() and
is.real() has been moved to ‘defunct’ and the
functions removed.
The maxRasters argument of pdf() (unused since
R 2.14.0) has been removed.
The unused fontsmooth argument has been removed from
the quartz() device.
All the (non-API) EISPACK entry points in R have been removed.
chol(pivot = TRUE, LINPACK = TRUE) is deprecated.
The long-deprecated use of \synopsis in the
Usage section of ‘.Rd’ files will be removed in R
3.1.0.
.find.package() and .path.package() are
deprecated: only the public versions without the dot have ever
been in the API.
In a package's ‘DESCRIPTION’ file,
License: X11is deprecated, since it includes ‘Copyright (C) 1996 X Consortium’ which cannot be appropriate for a current R package. Use ‘MIT’ or ‘BSD_2_clause’ instead.
The C code underlying base graphics has been migrated to the
graphics package (and hence no longer uses
.Internal() calls).
Most of the .Internal() calls used in the stats
package have been migrated to C code in that package.
This means that a number of .Internal() calls which have
been used by packages no longer exist, including
.Internal(cor) .Internal(cov),
.Internal(optimhess) and .Internal(update.formula).
Some .External() calls to the base package
(really to the R executable or shared library) have been moved to
more appropriate packages. Packages should not have been using
such calls, but some did (mainly those used by integrate()).
There is a new function mcaffinity() which allows
getting or setting the CPU affinity mask for the current R process on
systems that supports this (currently only Linux has been tested
successfully). It has no effect on systems which do not support
process affinity. Users are not expected to use this function
directly (with the exception of fixing libraries that break
affinity settings like OpenBLAS) – the function is rather
intended to support affinity control in high-level parallel
functions. In the future, R may supplement lack of affinity
control in the OS by its own bookkeeping via mcaffinity()
related to processes and threads it spawns.
mcparallel() has a new argument mc.affinity
which attempts to set the affinity of the child process according
to the specification contained therein.
The port used by socket clusters is chosen randomly: this
should help to avoid clashes observed when two users of a
multi-user machine try to create a cluster at the same time. To
reproduce the previous behaviour set environment variable
R_PARALLEL_PORT to 10187.
There has been some minor re-organization of the non-API header files. In particular, ‘Rinternals.h’ no longer includes the non-API header ‘R_exts/PrtUtil.h’, and that no longer includes ‘R_exts/Print.h’.
Passing NULL to .C() is now an error.
.C() and .Fortran() now warn if
"single" arguments are used with DUP = FALSE, as
changes to such arguments are not returned to the caller.
C entry points R_qsort and R_qsort_I now have
start and end as size_t to allow them to work
with longer vectors on 64-bit platforms. Code using them should
be recompiled.
A few recently added C entry points were missing the
remapping to Rf_, notably [dpq]nbinom_mu.
Some of the interface pointers formerly available only to
R.app are now available to front-ends on all
Unix-alikes: one has been added for the interface to
View().
PACKAGE = "" is now an error in .C() etc calls:
it was always contrary to the documentation.
Entry point rcont2 has been migrated to package
stats and so is no longer available.
R_SVN_REVISION in ‘Rversion.h’ is now an integer
(rather than a string) and hence usable as e.g.
#if R_SVN_REVISION < 70000.
The entry points rgb2hsv and hsv2rgb have been
migrated to package grDevices and so are no longer available.
R_GE_version has been increased to 10 and
name2col removed (use R_GE_str2col instead). R
internal colour codes are now defined using the typedef
rcolor.
The REPROTECT macro now checks that the protect index
is valid.
Several non-API entry points no longer used by R have been
removed, including the Fortran entry points chol,
chol2inv, cg, ch and rg, and the C
entry points Brent_fmin, fft_factor and fft_work.
If a .External call is registered with a number of
arguments (other than -1), the number of arguments passed
is checked for each call (as for other foreign function calls).
It is now possible to write custom connection implementations outside core R using ‘R_ext/Connections.h’. Please note that the implementation of connections is still considered internal and may change in the future (see the above file for details).
The management of translations has been converted to R
code: see ?tools::update_pkg_po.
The translations for the R interpreter and
RGui.exe are now part of the base package (rather than
having sources in directory ‘po’ and being installed to
‘share/locale’). Thus the base package supports three
translation domains, R-base, R and RGui.
The compiled translations which ship with R are all
installed to the new package translations for easier
updating. The first package of that name found on
.libPaths() at the start of the R session will be used.
(It is possible messages will be used before .libPaths() is
set up in which case the default translations will be used: set
environment variable R_TRANSLATIONS to point to the location
of the intended translations package to use this right from
the start.)
The translations form a separate group in the Windows installer, so can be omitted if desired.
The markup for many messages has been changed to make them easier to translate, incorporating suggestions from Łukasz Daniel.
There is again support for building without using the C
‘long double’ type. This is required by C99, but system
implementations can be slow or flawed. Use configure
option --disable-long-double.
make pdf and make install-pdf now make
and install the full reference index (including all base and
recommended packages).
The 'reference manual' on the Windows GUI menu and included in the installer is now the full reference index, including all base and recommended packages.
R help pages and manuals have no ISBNs because ISBN rules no longer allow constantly changing content to be assigned an ISBN.
The Windows installer no longer installs a Start Menu link to the static help pages; as most pages are generated dynamically, this led to a lot of broken links.
Any custom settings for Java configuration are recorded in
file ‘etc/javaconf’ for subsequent use by R CMD
javareconf.
There is now support for makeinfo version 5.0
(which requires a slightly different ‘.texi’ syntax).
The minimum versions for --use-system-zlib and
--use-system-pcre are now tested as 1.2.5 and 8.10
respectively.
On Windows, the stack size is reduced to 16MB on 32-bit systems: misguided users were launching many threads without controlling the stack size.
configure no longer looks for file
‘~/.Rconfig’: ‘~/.R/config’ has long been preferred.
When R CMD build is run in an encoding other than
the one specified in the package's ‘DESCRIPTION’ file it
tries harder to expand the authors@R field in the specified
encoding. (PR#14958)
If R CMD INSTALL is required to expand the
authors@R field of the ‘DESCRIPTION’ file, it tries
harder to do so in the encoding specified for the package (rather
than using ASCII escapes).
Fix in package grid for pushing a viewport into a layout cell, where the layout is within a viewport that has zero physical width OR where the layout has zero total relative width (likewise for height). The layout column widths (or row heights) in this case were being calculated with non-finite values. (Reported by Winston Chang.)
solve(A, b) for a vector b gave the answer
names from colnames(A) for LINPACK = TRUE but not in
the default case.
La.svd() accepts logical matrices (as documented, and
as svd() did).
legend() now accepts negative pch values, in
the same way points() long has.
Parse errors when installing files now correctly display the name of the file containing the bad code.
In Windows, tcltk windows were not always properly constructed. (PR#15150)
The internal functions implementing parse(),
tools::parseLatex() and tools::parse_Rd() were not
reentrant, leading to errors in rare circumstances such as a
garbage collection triggering a recursive call.
Field assignments in reference class objects via
$<- were not being checked
because the magic incantation to turn methods on for that
primitive operator had been inadvertently omitted.
setHook(hookname, value, action="replace") set the
hook to be the value, rather than a list containing the value as
documented. (PR#15167)
If a package used a ‘NEWS.Rd’ file, the main HTML package index page did not link to it. (Reported by Dirk Eddelbuettel.)
The primitive implementation of @<- was not
checking the class of the replacement. It now does a check,
quicker but less general than slot<-. See the help.
split(x, f) now recycles classed objects x in
the same way as vectors. (Reported by Martin Morgan.)
pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE)
is no longer -Inf; ditto for corresponding pt() and
pf() calls, such as pt(45, df=5000, lower.tail=FALSE,
log.p=TRUE). (PR#15162)
The Windows graphics device would crash R if a user attempted to load the graphics history from a variable that was not a saved history. (PR#15230)
The workspace size for the predict()
method for loess() could exceed the maximum integer size.
(Reported by Hiroyuki Kawakatsu.)
ftable(x, row.vars, col.vars) now also works when the
*.vars arguments are (integer or character vectors) of
length zero.
Calling cat() on a malformed UTF-8 string could cause
the Windows GUI to lock up. (PR#15227)
removeClass(cc) gave "node stack overflow" for some
class definitions containing "array" or "matrix".
CHANGES IN R VERSION 2.15.3lgamma(x) for very small x (in the
denormalized range) is no longer Inf with a warning.
image() now sorts an unsorted breaks vector,
with a warning.
The internal methods for tar() and untar() do
a slightly more general job for ‘ustar’-style handling of
paths of more than 100 bytes.
Packages compiler and parallel have been added to the reference index (‘refman.pdf’).
untar(tar = "internal") has some support for
pax headers as produced by e.g. gnutar --posix
(which seems prevalent on OpenSUSE 12.2) or
bsdtar --format pax, including long path and link names.
sQuote() and dQuote() now handle 0-length
inputs. (Suggestion of Ben Bolker.)
summaryRprof() returns zero-row data frames rather
than throw an error if no events are recorded, for consistency.
The included version of PCRE has been updated to 8.32.
The tcltk namespace can now be re-loaded after unloading.
The Tcl/Tk event loop is inhibited in a forked child from package
parallel (as in e.g. mclapply()).
parallel::makeCluster() recognizes the value
random for the environment variable R_PARALLEL_PORT:
this chooses a random value for the port and reduces the chance of
conflicts when multiple users start a cluster at the same time.
The default for TAR on Windows for R CMD
build has been changed to be internal if no
tar command is on the path.
This enables most packages to be built ‘out of the box’
without Rtools: the main exceptions are those which need
to be installed to re-build vignettes and need Rtools
for installation (usually because they contain compiled code).
On a 64-bit Windows platform with enough RAM, R_alloc
can now allocate up to just under 32GB like other 64-bit
platforms.
Use of col2rgb(0) is deprecated (see the help page
for its limitations).
The deprecated intensities component returned by
hist() is no longer recognized by the plot() method
and will be removed in R 3.0.0.
real(), as.real() and is.real() are now
formally deprecated and give a warning.
This is formal notice that the non-API EISPACK entry points in R will be removed shortly.
The configure tests for Objective C and Objective
C++ now work on Mac OS 10.8 with Xcode 4.5.2 (PR#15107).
The cairo-based versions of X11() now work with
current versions of cairographics (e.g. 1.12.10). (PR#15168)
A workaround for earlier versions of R is to use
X11.options(type = "nbcairo").
Configuration and R CMD javareconf now come up
with a smaller set of library paths for Java on Oracle-format JDK
(including OpenJDK). This helps avoid conflicts between libraries
(such as libjpeg) supplied in the JDK and system
libraries. This can always be overridden if needed: see the
‘R Installation and Administration’ manual.
beta(a, b) could overflow to infinity in its
calculations when one of a and b was less than one.
(PR#15075)
lbeta(a, b) no longer gives NaN if a or
b is very small (in the denormalized range).
bquote() is now able to substitute default arguments in
single-argument functions. (PR#15077)
browseEnv(html = FALSE) would segfault if called from
R (not R.app) on a CRAN-style Mac OS X build of R.
[[<- for lists (generic vectors) needed to increment
NAMED count when RHS is used more than once. (PR#15098)
On Windows, warnings about opening a file or pipe with a non-ASCII description were sometimes output in UTF-8 rather than in the current locale's character set.
The call() function did not duplicate its arguments.
(PR#15115)
TukeyHSD() could give NA results with some
na.action methods such as na.exclude().
(Hinted at on R-help by John Fox.)
The deprecated svd(X, LINPACK = TRUE) could alter
X in R 2.15.[12]. (Reported by Bill Dunlap.)
Under Windows, file.link() and file.symlink()
used the link name twice, so would always fail. (Reported
by Rui Barradas/Oliver Soong).
summaryRprof(memory = "both") mixed up the units of
Vcells and Ncells: it now works in bytes. (PR#15138)
tools::Rd2HTML() would sometimes delete text. (PR#15134)
plot() failed for "table" objects containing
just one entry. (PR#15118)
embedFonts() needed to quote some filepaths.
(PR#15149)
parallel::mccollect() handled NULL returns
incorrectly (removing the element rather than setting it to
NULL).
The full reference index (‘fullrefman.pdf’) was missing packages compiler and parallel.
The report for
optim(method = "L-BFGS-B", control = list(trace = 1))
reported the last completed and not the current iteration, unlike
other methods and trace levels. (PR#15103)
qt(1e-12, 1.2) no longer gives NaN.
dt(1e160, 1.2, log=TRUE) no longer gives -Inf.
On Windows the untar() function now quotes the
directory name when using an external tar utility, so
R CMD check will handle pathnames containing spaces.
The version for Windows 8 and Windows Server 2012 is now
displayed by win.version(). (Reported by Gabor
Grothendieck.)
The custom Windows installer target myR in the
installer ‘Makefile’ did not work in 2.15.2. (Reported
by Erich Neuwirth.)
aperm(matrix(1:6, 2, dimnames=list(A={}, B={})), "A")
no longer segfaults.
Expressions involving user defined operators were not always deparsed faithfully. (PR#15179)
The enc2utf8() function converted NA_character_
to "NA" in non-UTF-8 locales. (PR#15201)
The exclude argument to xtabs() was ignored
for "factor" arguments.
On Windows, work around an event-timing problem when the RGui console was closed from the ‘X’ control and the closure cancelled. (This would on some 64-bit systems crash R, typically those with a slow GPU relative to the CPU.)
On unix Rscript will pass the r_arch setting
it was compiled with on to the R process so that the architecture
of Rscript and that of R will match unless overridden.
On Windows, basename(), dirname() and
file.choose() have more support for long non-ASCII file
names with 260 or more bytes when expressed in UTF-8.
CHANGES IN R VERSION 2.15.2 The X11() window gains an icon: the
latter may be especially useful on Ubuntu's ‘Unity’
interface.
The WM_CLASS should be set in circumstances where the
Window Manager failed to make use of X11 resource settings.
(Contributed by Philip Johnson.)
The "Date" and "POSIXt" methods for
cut() will accept an unsorted breaks argument (as
the default method does, although this was undocumented).
(Wish of PR#14961.)
Reference class methods (in the methods package) that
use other methods in an indirect way (e.g., by sapply())
must tell the code analysis to include that method. They can now
do so by invoking $usingMethods().
More Polish translations are available: for the
RGui menus and for several recommended packages.
Multistratum MANOVA works. In fact, it seems to have done so for years in spite of the help page claiming it did not.
qqline() has new optional arguments
distribution, probs and qtype, following the
example of lattice's panel.qqmathline().
The handling of single quotes in the en@quot
pseudo-language has been slightly improved. Double quotes are no
longer converted.
New functions checkPoFiles() and checkPoFile()
have been added to the tools package to check for
consistency of format strings in translation files.
model.matrix(~1, ...) now also contains the same
rownames that less trivial formulae produce. (Wish of PR#14992,
changes the output of several packages.)
Misuse of rep() on undocumented types of objects
(e.g. calls) is now reported as an error.
The included LAPACK has been updated to 3.4.1, with some patches from the current SVN sources. (Inter alia, this resolves PR#14692.)
file.copy(recursive = TRUE) has some additional
checks on user error leading to attempted infinite recursion (and on
some platforms to crashing R).
PCRE has been updated to version 8.31, a bug-fix release.
The included version of liblzma has been updated to
version 5.0.4, a minor bug-fix release.
New function .bincode(), a ‘bare-bones’
version of cut.default(labels = FALSE) for use in packages
with image() methods.
The HTML manuals now use directional single quotes.
maintainer() now converts embedded new lines to
spaces. It no longer gives a non-obvious error for non-installed
packages.
The X11() device has some protection against
being used with forked processes via package parallel.
Setting the environment variable R_OSX_VALGRIND (to
any value) allows R to be run under valgrind on Mac OS
10.6 and 10.7 (valgrind currently has very limited
support for 10.8), provided system() is not used (directly
or indirectly). This should not be needed for valgrind
>= 3.8.1.
The model.frame() method for "lm" uses
xlevels: this is safer if data was supplied or
model = FALSE was used and the levels of factors used in
the fit had been re-ordered since fitting.
Similarly, model.frame(fm, data=<data>) copies across
the variables used for safe prediction from the fit.
Functions such as parLapply() in package
parallel can make use of a default cluster if one is set.
(Reported by Martin Morgan.)
chol(pivot = TRUE, LINPACK = FALSE) is now available
using LAPACK 3.2 subroutine DPSTRF.
The functions .C(), .Call(),
.External() and .Fortran() now check that they are
called with an unnamed first argument: the formal arguments were
changed from name= to .NAME= in R 2.13.0, but some
packages were still using the old name. This is currently a
warning, but will be an error in future.
step() no longer tries to improve a model with
AIC of -Inf (a perfect fit).
spline() and splinefun() gain a new method
"hyman", an implementation of Hyman's method of
constructing monotonic interpolation splines. (Based on
contributions of Simon Wood and Rob Hyndman.)
On Windows, the C stack size has been increased to 64MB (it has been 10MB since the days of 32MB RAM systems).
array() is now implemented in C code (for speed) when
data is atomic or an unclassed list (so it is known that
as.vector(data) will have no class to be used by rep()).
rep() is faster and uses less memory,
substantially so in some common cases (e.g. if times is of
length one or length.out is given, and each = 1).
findInterval(), tabulate(), cut(),
hist() and image.default() all use .Call()
and are more efficient.
duplicated(), unique() and similar now
support vectors of lengths above 2^29 on 64-bit
platforms.
Omitting PACKAGE in .C() etc calls was
supposed to make use of the DLL from the namespace within which
the enclosing function was defined. It was less successful in
doing so than it might be, and gave no indication it had failed.
A new search strategy is very successful and gives a warning
when it fails. In most cases this is because the entry point is
not actually provided by that package (and so PACKAGE
should be used to indicate which package is intended) but in some
the namespace does not have a DLL specified by a
useDynLib() directive so PACKAGE is required.
R CMD check now checks if a package can be loaded
by library(pkgname, lib.loc = "somewhere") without being on
the library search path (unless it is already installed in
.Library, when it always will be).
R CMD check --as-cran notes ‘hidden’ files
and directories (with names starting with a dot) that are not
needed for the operation of R CMD INSTALL or R CMD
build: such files should be excluded from the published tarball.
R CMD check (if checking subdirectories) checks
that the R code in any demos is ASCII and can be parsed, and
warns if not.
When R CMD Rd2pdf is used with ‘inputenx.sty’,
it allows further characters (mainly for Eastern European
languages) by including ‘ix-utf8enc.dfu’ (if available).
(Wish of PR#14989.)
R CMD build now omits several types of hidden
files/directories, including ‘inst/doc/.Rinstignore’,
‘vignettes/.Rinstignore’, (‘.Rinstignore’ should be at
top level), ‘.deps’ under ‘src’, ‘.Renviron’,
‘.Rprofile’, ‘.Rproj.user’, ‘.backups’,
‘.cvsignore’, ‘.cproject’, ‘.directory’,
‘.dropbox’, ‘.exrc’, ‘.gdb.history’,
‘.gitattributes’, ‘.gitignore’, ‘.gitmodules’,
‘.hgignore’, ‘.hgtags’, ‘.htaccess’,
‘.latex2html-init’, ‘.project’, ‘.seed’,
‘.settings’, ‘.tm_properties’ and various leftovers.
R CMD check now checks for .C(),
.Call(), .External() and .Fortran() calls in
other packages, and gives a warning on those found from R itself
(which are not part of the API and change without notice: many
will be changed for R 3.0.0).
The limit for R_alloc on 64-bit platforms has been
raised to just under 32GB (from just under 16GB).
The misuse of .C("name", ..., PACKAGE = foo) where
foo is an arbitrary R object is now an error.
The misuse .C("name",..., PACKAGE = "") is now warned about
in R CMD check, and will be an error in future.
Use of array() with a 0-length dim argument is
deprecated with a warning (and was contrary to the documentation).
Use of tapply() with a 0-length INDEX list is
deprecated with a warning.
Translation packages are deprecated.
Calling rep() or rep.int() on a pairlist is
deprecated and will give a warning. In any case, rep()
converted a pairlist to a list so you may as well do that
explicitly.
Entry point rcont2 is no longer part of the API, and
will move to package stats in R 3.0.0.
The ‘internal’ graphics device invoked by
.Call("R_GD_nullDevice", package = "grDevices") is about to
be removed: use pdf(file = NULL) instead.
eigen(EISPACK = TRUE),
chol(pivot = FALSE, LINPACK = TRUE),
chol2inv(LINPACK = TRUE), solve(LINPACK = TRUE) and
svd(LINPACK = TRUE) are deprecated and give a warning.
They were provided for compatibility with R 1.7.0 (Mar 2003)!
The ‘internal function’ kappa.tri() has been
renamed to .kappa_tri() so it is not inadvertently called
as a method for class "tri".
Functions sessionData() and browseAll() in
package methods are on a help page describing them as
‘deprecated’ and are now formally deprecated.
For a Windows or Mac OS X binary package install,
install.packages() will check if a source package is
available on the same repositories, and report if it is a later
version or there is a source package but no binary package
available.
This check can be suppressed: see the help page.
install.packages(type = "both") has been enhanced.
In interactive use it will ask whether to choose the source
version of a package if the binary version is older and contains
compiled code, and also asks if source packages with no binary
version should be installed).
There is a new configure option
--with-libtiff (mainly in case the system installation
needs to be avoided).
LAPACK 3.4.1 does use some Fortran 90 features, so
g77 no longer suffices.
If an external LAPACK is used, it must be version 3.2 or later.
On Windows, starting Rterm via R.exe
caused Ctrl-C to misbehave. (PR#14948)
The tools::latexToUtf8() function missed conversions that
were contained within braces.
Long timezone specifications (such as a file name preceded
by :) could crash as.POSIXlt. (PR#14945)
R CMD build --resave-data could fail if there was no
‘data’ directory but there was an ‘R/sysdata.rda’ file.
(PR#14947)
is.na() misbehaved on a 0-column data frame.
(PR#14959)
anova.lmlist() failed if test was
supplied. (PR#14960)
It was unable to compute Cp tests for object of class "lm"
(it assumed class "glm").
The formula method for sunflowerplot() now
allows xlab and ylab to be set. (Reported by Gerrit
Eichner.)
The "POSIXt" and "Date" methods for hist()
could fail on Windows where adjustments to the right-hand boundary
crossed a DST transition time.
On Windows, the code in as.POSIXct() to handle
incorrectly specified isdst fields might have resulted in
NA being returned.
aov() and manova() gave spurious warning about
singular error model in the multiresponse case.
In ns() and bs(), specifying knots = NULL
is now equivalent to omitting it, also when df is
specified. (PR#14970)
sprintf() did not accept numbered arguments ending
in zero. (PR#14975)
rWishart() could overflow the C stack and maybe crash
the R process for dimensions of several hundreds or more.
(Reported by Michael Braun on R-sig-mac.)
Base package vignettes (e.g. vignette("Sweave")) were
not fully installed in builds of R from the tarball.
lchoose() and choose() could overflow the C
stack and crash R.
When given a 0-byte file and asked to keep source
references, parse() read input from stdin()
instead.
pdf(compress = TRUE) did not delete temporary files
it created until the end of the R session. (PR#14991)
logLik() did not detect the error of applying it
to a multiple-response linear model. (PR#15000)
file.copy(recursive = TRUE) did not always report
FALSE for a failure two or more directories deep.
qgeom() could return -1 for extremely small
q. (PR#14967)
smooth.spline() used DUP = FALSE which allowed
its compiled C code to change the function: this was masked by the
default byte-compilation. (PR#14965)
In Windows, the GUI preferences for foreground color were not always respected. (Reported by Benjamin Wells.)
On OS X, the Quartz versions of the bitmap devices did not
respect antialias = "none". (PR#15006)
unique() and similar would infinite-loop if called on
a vector of length > 2^29 (but reported that the
vector was too long for 2^30 or more).
parallel::stopCluster() now works with MPI
clusters without snow being on the search path.
terms.formula() could exhaust the stack, and the
stack check did not always catch this before the segfault.
(PR#15013)
sort.list(method = "radix") could give incorrect
results on certain compilers (seen with clang on Mac OS
10.7 and Xcode 4.4.1).
backsolve(T, b) gave incorrect results when
nrows(b) > ncols(T) and b had more than one column.
It could segfault or give nonsense if k was specified as
more than ncols(T).
smooth.spline() did not check that a specified
numeric spar was of length 1, and gave corrupt results if
it was of length 0.
Protection added to do_system. (PR#15025)
Printing of vectors with names > 1000 characters now works correctly rather than truncating. (PR#15028)
qr() for a complex matrix did not pivot the column names.
--with-blas='-framework vecLib' now also works on OS X 10.8.
R CMD check no longer fails with an error if
a ‘DESCRIPTION’ file incorrectly contains a blank line.
(Reported by Bill Dunlap.)
install.packages(type = "both") could call
chooseCRANmirror() twice.
lm.wfit() could segfault in R 2.15.1 if all the
weights were zero. (PR#15044)
A malformed package name could cause R CMD INSTALL
to write outside the target library.
Some of the quality control functions
(e.g. tools::checkFF()) were wrongly identifying the source
of S4 methods in a package and so not checking them.
The default type of display by browseEnv() when using
R.app on Mac OS X has been incorrect for a long time.
The implementation of importMethodsFrom in a
NAMESPACE file could be confused and fail to find generics
when importing from multiple packages (reported and fixed by
Michael Lawrence).
The detection of the C stack direction is better protected against compiler optimization. (PR#15011)
Long custom line types would sometimes segfault on the cairographics-based devices. (PR#15055)
tools::checkPoFile() unprotected too early in its C
code and so segfaulted from time to time.
The Fortran code underlying nlminb() could
infinite-loop if any of the input functions returned NA or
NaN. This is now an error for the gradient or Hessian, and
a warning for the function (with the value replaced by
Inf). (In part, PR#15052.)
The code for creating coerce() methods could
generate false notes about ambiguous selection; the notes have
been suppressed for this function.
arima.sim() could give too long an output in some
corner cases (in part, PR#15068).
anova.glm() with test = "Rao" didn't work when
models included an offset. (Reported by Søren Feodor Nielsen.)
as.data.frame.matrix() could return invalid data
frame with no row.names attribute for 0-row matrix. (Reported
by Hervé Pagès.)
Compilation with the vecLib or Accelerate
frameworks on OS X without using that also for LAPACK is more
likely to be successful.
CHANGES IN R VERSION 2.15.1source() now uses withVisible() rather than
.Internal(eval.with.vis). This sometimes alters tracebacks
slightly.
install.packages("pkg_version.tgz") on Mac OS X now
has sanity checks that this is actually a binary package (as
people have tried it with incorrectly named source packages).
splineDesign() and spline.des() in package
splines have a new option sparse which can be used
for efficient construction of a sparse B-spline design matrix
(via Matrix).
norm() now allows type = "2" (the
‘spectral’ or 2-norm) as well, mainly for didactical
completeness.
pmin() and pmax()) now also work when one of
the inputs is of length zero and others are not, returning a
zero-length vector, analogously to, say, +.
colorRamp() (and hence colorRampPalette()) now
also works for the boundary case of just one color when the ramp is
flat.
.C() gains some protection against the misuse of
character vector arguments. (An all too common error is to pass
character(N), which initializes the elements to "",
and then attempt to edit the strings in-place, sometimes forgetting
to terminate them.)
Calls to the new function globalVariables() in
package utils declare that functions and other objects in a
package should be treated as globally defined, so that CMD
check will not note them.
print(packageDescription(*)) trims the Collate
field by default.
The included copy of zlib has been updated to version
1.2.7.
A new option "show.error.locations" has been added.
When set to TRUE, error messages will contain the
location of the most recent call containing source reference
information. (Other values are supported as well; see
?options.)
The NA warning messages from e.g. pchisq() now report
the call to the closure and not that of the .Internal.
Added Polish translations by Łukasz Daniel.
In package parallel, makeForkCluster() and the
multicore-based functions use native byte-order for serialization
(deferred from 2.15.0).
lm.fit(), lm.wfit(), glm.fit() and
lsfit() do less copying of objects, mainly by using
.Call() rather than .Fortran().
.C() and .Fortran() do less copying: arguments
which are raw, logical, integer, real or complex vectors and are
unnamed are not copied before the call, and (named or not) are not
copied after the call. Lists are no longer copied (they are
supposed to be used read-only in the C code).
tabulate() makes use of .C(DUP = FALSE) and
hence does not copy bin. (Suggested by Tim Hesterberg.)
It also avoids making a copy of a factor argument bin.
Other functions (often or always) doing less copying include
cut(), dist(), the complex case of eigen(),
hclust(), image(), kmeans(), loess(),
stl() and svd(LINPACK = TRUE).
There is less copying when using primitive replacement
functions such as names(), attr() and
attributes().
The converters for use with .C() (see
?getCConverterDescriptions) are deprecated: use the
.Call() interface instead. There are no known examples
(they were never fully documented).
For R CMD check, a few people have reported
problems with junctions on Windows (although they were tested on
Windows 7, XP and Server 2008 machines and it is unknown under
what circumstances the problems occur). Setting the environment
variable R_WIN_NO_JUNCTIONS to a non-empty value (e.g. in
‘~/.R/check.Renviron’) will force copies to be used instead.
R CMD INSTALL with _R_CHECK_INSTALL_DEPENDS_
set to a true value (as done by R CMD check --as-cran)
now restricts the packages available when lazy-loading as well
as when test-loading (since packages such as ETLUtils
and agsemisc had top-level calls to library()
for undeclared packages).
This check is now also available on Windows.
C entry points mkChar and mkCharCE now check
that the length of the string they are passed does not exceed
2^31-1 bytes: they used to overflow with
unpredictable consequences.
C entry points R_GetCurrentSrcref and
R_GetSrcFilename have been added to the API to allow
debuggers access to the source references on the stack.
Windows-specific changes will now be announced in this file (‘NEWS’). Changes up and including R 2.15.0 remain in the ‘CHANGES’ file.
There are two new environment variables which control the defaults for command-line options.
If R_WIN_INTERNET2 is set to a non-empty value, it is as if --internet2 was used.
If R_MAX_MEM_SIZE is set, it gives the default memory limit if --max-mem-size is not specified: invalid values being ignored.
lsfit() lost the names from the residuals.
More cases in which merge() could create a data frame
with duplicate column names now give warnings. Cases where
names specified in by match multiple columns are errors.
Nonsense uses such as seq(1:50, by = 5) (from package
plotrix) and seq.int(1:50, by = 5) are now errors.
The residuals in the 5-number summary printed by
summary() on an "lm" object are now explicitly
labelled as weighted residuals when non-constant weights are
present. (Wish of PR#14840.)
tracemem() reported that all objects were copied
by .C() or .Fortran() whereas only some object types
were ever copied.
It also reported and marked as copies some transformations
such as rexp(n, x): it no longer does so.
The plot() method for class "stepfun" only
used the optional xval argument to compute xlim and
not the points at which to plot (as documented). (PR#14864)
Names containing characters which need to be escaped were not deparsed properly. (PR#14846)
Trying to update (recommended) packages in
‘R_HOME/library’ without write access is now dealt with more
gracefully. Further, such package updates may be skipped (with a
warning), when a newer installed version is already going to be
used from .libPaths(). (PR#14866)
hclust() is now fast again (as up to end of 2003),
with a different fix for the "median"/"centroid" problem. (PR#4195).
get_all_vars() failed when the data came entirely
from vectors in the global environment. (PR#14847)
R CMD check with _R_CHECK_NO_RECOMMENDED_
set to a true value (as done by the --as-cran option)
could issue false errors if there was an indirect dependency
on a recommended package.
formatC() uses the C entry point str_signif
which could write beyond the length allocated for the output string.
Missing default argument added to implicit S4 generic for
backsolve(). (PR#14883)
Some bugs have been fixed in handling load actions that
could fail to export assigned items or generate spurious warnings
in CMD check on loading.
For tiff(type = "windows"), the numbering of per-page
files except the last was off by one.
On Windows, loading package stats (which is done for
a default session) would switch line endings on ‘stdout’
and ‘stderr’ from CRLF to LF. This affected
Rterm and R CMD BATCH.
On Windows, the compatibility function x11() had
not kept up with changes to windows(), and issued
warnings about bad parameters. (PR#14880)
On Windows, the Sys.glob() function did not handle
UNC paths as it was designed to try to do. (PR#14884)
In package parallel, clusterApply() and similar
failed to handle a (pretty pointless) length-1 argument. (PR#14898)
Quartz Cocoa display reacted asynchronously to
dev.flush() which means that the redraw could be performed
after the plot has been already modified by subsequent code. The
redraw is now done synchronously in dev.flush() to allow
animations without sleep cycles.
Source locations reported in traceback() were
incorrect when byte-compiled code was on the stack.
plogis(x, lower = FALSE, log.p = TRUE) no longer
underflows early for large x (e.g. 800).
?Arithmetic's “1 ^ y and y ^ 0
are 1, always” now also applies for integer
vectors y.
X11-based pixmap devices like png(type = "Xlib") were
trying to set the cursor style, which triggered some warnings and
hangs.
Code executed by the built-in HTTP server no longer allows other HTTP clients to re-enter R until the current worker evaluation finishes, to prevent cascades.
The plot() and Axis() methods for class
"table" now respect graphical parameters such as
cex.axis. (Reported by Martin Becker.)
Under some circumstances package.skeleton() would
give out progress reports that could not be translated and so were
displayed by question marks. Now they are always in English.
(This was seen for CJK locales on Windows, but may have occurred
elsewhere.)
The evaluator now keeps track of source references outside
of functions, e.g. when source() executes a script.
The replacement method for window() now works
correctly for multiple time series of class "mts".
(PR#14925)
is.unsorted() gave incorrect results on non-atomic
objects such as data frames. (Reported by Matthew Dowle.)
The value returned by tools::psnice() for invalid
pid values was not always NA as documented.
Closing an X11() window while locator() was
active could abort the R process.
getMethod(f, sig) produced an incorrect error message
in some cases when f was not a string).
Using a string as a “call” in an error condition
with options(showErrorCalls=TRUE) could cause a segfault.
(PR#14931)
The string "infinity" allowed by C99 was not accepted
as a numerical string value by e.g. scan() and
as.numeric(). (PR#14933)
In legend(), setting some entries of lwd to
NA was inconsistent (depending on the graphics device) in
whether it would suppress those lines; now it consistently does
so. (PR#14926)
by() failed for a zero-row data frame. (Reported by
Weiqiang Qian.)
The Yates' correction in chisq.test() could be bigger
than the terms it corrected, previously leading to an infinite
test statistic in some corner cases which are now reported as
NaN.
xgettext() and related functions sometimes returned
items that were not strings for translation. (PR#14935)
plot(<lm>, which=5) now correctly labels the factor
level combinations for the special case where all
h[i,i] are the same. (PR#14837)
Sys.glob() caused a segfault if the first element of
path was NA_character. (PR#14990)
CHANGES IN R VERSION 2.15.0 The behaviour of unlink(recursive = TRUE) for a
symbolic link to a directory has changed: it now removes the link
rather than the directory contents (just as rm -r does).
On Windows it no longer follows reparse points (including junctions and symbolic links).
Environment variable RD2DVI_INPUTENC has been renamed to RD2PDF_INPUTENC.
.Deprecated() becomes a bit more flexible, getting an
old argument.
Even data-only packages without R code need a namespace and so may need to be installed under R 2.14.0 or later.
assignInNamespace() has further restrictions on use
apart from at top-level, as its help page has warned.
Expect it to be disabled from programmatic use in the future.
system() and system2() when capturing output
report a non-zero status in the new "status" attribute.
kronecker() now has an S4 generic in package
methods on which packages can set methods. It will be
invoked by X %x% Y if either X or Y is an S4
object.
pdf() accepts forms like file = "|lpr" in the
same way as postscript().
pdf() accepts file = NULL.
This means that the device does NOT create a PDF file
(but it can still be queried, e.g., for font metric info).
format() (and hence print()) on
"bibentry" objects now uses options("width") to
set the output width.
legend() gains a text.font argument. (Suggested
by Tim Paine, PR#14719.)
nchar() and nzchar() no longer accept factors
(as integer vectors). (Wish of PR#6899.)
summary() behaves slightly differently (or more
precisely, its print() method does). For numeric inputs, the
number of NAs is printed as an integer and not a real. For dates
and datetimes, the number of NAs is included in the printed output
(the latter being the wish of PR#14720).
The "data.frame" method is more consistent with the default
method: in particular it now applies zapsmall() to
numeric/complex summaries.
The number of items retained with options(warn = 0)
can be set by options(nwarnings=).
There is a new function assignInMyNamespace() which
uses the namespace of the function it is called from.
attach() allows the default name for an attached file
to be overridden.
bxp(), the work horse of boxplot(), now uses a
more sensible default xlim in the case where at is
specified differently from 1:n, see the discussion on R-devel,
https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html.
New function paste0(), an efficient version of
paste(*, sep=""), to be used in many places for more
concise (and slightly more efficient) code.
Function setClass() in package methods now
returns, invisibly, a generator function for the new class,
slightly preferred to calling new(), as explained on the
setClass help page.
The "dendrogram" method of str() now takes
its default for last.str from option str.dendrogram.last.
New simple fitted() method for "kmeans" objects.
The traceback() function can now be called with
an integer argument, to display a current stack trace. (Wish of
PR#14770.)
setGeneric() calls can be simplified when creating
a new generic function by supplying the default method as the
def argument. See ?setGeneric.
serialize() has a new option xdr = FALSE which
will use the native byte-order for binary serializations. In
scenarios where only little-endian machines are involved (these
days, close to universal) and (un)serialization takes an
appreciable amount of time this may speed up noticeably
transferring data between systems.
The internal (un)serialization code is faster for long vectors, particularly with XDR on some platforms. (Based on a suggested patch by Michael Spiegel.)
For consistency, circles with zero radius are omitted by
points() and grid.circle(). Previously this was
device-dependent, but they were usually invisible.
NROW(x) and NCOL(x) now work whenever
dim(x) looks appropriate, e.g., also for more generalized
matrices.
PCRE has been updated to version 8.30.
The internal R_Srcref variable is now updated
before the browser stops on entering a function. (Suggestion of
PR#14818.)
There are ‘bare-bones’ functions .colSums(),
.rowSums(), .colMeans() and .rowMeans() for
use in programming where ultimate speed is required.
The formerly internal function
.package_dependencies() from package tools for
calculating (recursive) (reverse) dependencies on package databases
has been renamed to package_dependencies() and is now
exported.
There is a new function optimHess() to compute the
(approximate) Hessian for an optim() solution if
hessian = TRUE was forgotten.
.filled.contour() is a ‘bare-bones’ function to
add a filled-contour rectangular plot to an already prepared plot
region.
The stepping in debugging and single-step browsing modes has
changed slightly: now left braces at the start of the body are
stepped over for if statements as well as for for and
while statements. (Wish of PR#14814.)
library() no longer warns about a conflict with a
function from package:base if the function has the same
code as the base one but with a different environment. (An
example is Matrix::det().)
When deparsing very large language objects,
as.character() now inserts newlines after each line of
approximately 500 bytes, rather than truncating to the first
line.
New function rWishart() generates Wishart-distributed
random matrices.
Packages may now specify actions to be taken when the
package is loaded (setLoadActions()).
options(max.print = Inf) and similar now give an
error (instead of warnings later).
The "difftime" replacement method of units
tries harder to preserve other attributes of the argument. (Wish
of PR#14839.)
poly(raw = TRUE) no longer requires more unique
points than the degree. (Requested by John Fox.)
There is a new function mcmapply(), a parallel version
of mapply(), and a wrapper mcMap(), a parallel
version of Map().
A default cluster can be registered by the new function
setDefaultCluster(): this will be used by default in
functions such as parLapply().
clusterMap() has a new argument .scheduling to
allow the use of load-balancing.
There are new load-balancing functions parLapplyLB()
and parSapplyLB().
makePSOCKCluster() has a new option useXDR =
FALSE which can be used to avoid byte-shuffling for
serialization when all the nodes are known to be little-endian (or
all big-endian).
Non-ASCII vignettes without a declared encoding are no longer accepted.
C/C++ code in packages is now compiled with -NDEBUG
to mitigate against the C/C++ function assert being called
in production use. Developers can turn this off during package
development with PKG_CPPFLAGS = -UNDEBUG.
R CMD INSTALL has a new option --dsym
which on Mac OS X (Darwin) dumps the symbols alongside the
‘.so’ file: this is helpful when debugging with
valgrind (and especially when installing packages into
‘R.framework’). [This can also be enabled by setting the
undocumented environment variable PKG_MAKE_DSYM, since R
2.12.0.]
R CMD INSTALL will test loading under all installed
sub-architectures even for packages without compiled code, unless
the flag --no-multiarch is used. (Pure R packages can
do things which are architecture-dependent: in the case which
prompted this, looking for an icon in a Windows R executable.)
There is a new option install.packages(type = "both")
which tries source packages if binary packages are not available,
on those platforms where the latter is the default.
The meaning of install.packages(dependencies = TRUE)
has changed: it now means to install the essential dependencies of
the named packages plus the Suggests, but only the
essential dependencies of dependencies. To get the previous
behaviour, specify dependencies as a character vector.
R CMD INSTALL --merge-multiarch is now supported
on OS X and other Unix-alikes using multiple sub-architectures.
R CMD INSTALL --libs-only now by default does a
test load on Unix-alikes as well as on Windows: suppress with
--no-test-load.
R CMD check now gives a warning rather than a
note if it finds inefficiently compressed datasets. With
bzip2 and xz compression having been
available since R 2.10.0, it only exceptionally makes sense to
not use them.
The environment variable _R_CHECK_COMPACT_DATA2_ is no longer consulted: the check is always done if _R_CHECK_COMPACT_DATA_ has a true value (its default).
Where multiple sub-architectures are to be tested,
R CMD check now runs the examples and tests for all the
sub-architectures even if one fails.
R CMD check can optionally report timings on
various parts of the check: this is controlled by environment
variable _R_CHECK_TIMINGS_ documented in ‘Writing R
Extensions’. Timings (in the style of R CMD BATCH) are
given at the foot of the output files from running each test and
the R code in each vignette.
There are new options for more rigorous testing by
R CMD check selected by environment variables – see
the ‘Writing R Extensions’ manual.
R CMD check now warns (rather than notes) on
undeclared use of other packages in examples and tests:
increasingly people are using the metadata in the
‘DESCRIPTION’ file to compute information about packages,
for example reverse dependencies.
The defaults for some of the options in R CMD
check (described in the ‘R Internals’ manual) have
changed: checks for unsafe and .Internal() calls and
for partial matching of arguments in R function calls are now
done by default.
R CMD check has more comprehensive facilities for
checking compiled code and so gives fewer reports on entry points
linked into ‘.so’/‘.dll’ files from libraries
(including C++ and Fortran runtimes).
Checking compiled code is now done on FreeBSD (as well as the existing supported platforms of Linux, Mac OS X, Solaris and Windows).
R CMD build has more options for
--compact-vignettes: see R CMD build --help.
R CMD build has a new option --md5 to
add an ‘MD5’ file (as done by CRAN): this is used by R
CMD INSTALL to check the integrity of the distribution.
If this option is not specified, any existing (and probably stale) ‘MD5’ file is removed.
R CMD Rd2dvi is now defunct: use R CMD Rd2pdf.
Options such --max-nsize, --max-vsize and
the function mem.limits() are now defunct. (Options
--min-nsize and --min-vsize remain available.)
Use of library.dynam() without specifying all the
first three arguments is now disallowed.
Use of an argument chname in library.dynam()
including the extension ‘.so’ or ‘.dll’ (which was never
allowed according to the help page) is defunct. This also applies
to library.dynam.unload() and to useDynLib
directives in ‘NAMESPACE’ files.
The internal functions .readRDS() and
.saveRDS() are now defunct.
The off-line help() types "postscript" and
"ps" are defunct.
Sys.putenv(), replaced and deprecated in R 2.5.0, is
finally removed.
Some functions/objects which have been defunct for five or
more years have been removed completely. These include
.Alias(), La.chol(), La.chol2inv(),
La.eigen(), Machine(), Platform(),
Version, codes(), delay(),
format.char(), getenv(), httpclient(),
loadURL(), machine(), parse.dcf(),
printNoClass(), provide(), read.table.url(),
restart(), scan.url(), symbol.C(),
symbol.For() and unix().
The ENCODING argument to .C() is deprecated.
It was intended to smooth the transition to multi-byte character
strings, but can be replaced by the use of iconv() in the
rare cases where it is still needed.
Building with a positive value of --with-valgrind-instrumentation now also instruments logical, complex and raw vectors.
Passing R objects other than atomic vectors, functions,
lists and environments to .C() is now deprecated and will
give a warning. Most cases (especially NULL) are actually
coding errors. NULL will be disallowed in future.
.C() now passes a pairlist as a SEXP to the compiled
code. This is as was documented, but pairlists were in reality
handled differently as a legacy from the early days of R.
call_R and call_S are deprecated. They still
exist in the headers and as entry points, but are no longer
documented and should not be used for new code.
str(x, width) now obeys its width
argument also for function headers and other objects x
where deparse() is applied.
The convention for x %/% 0L for integer-mode x
has been changed from 0L to NA_integer_.
(PR#14754)
The exportMethods directive in a ‘NAMESPACE’
file now exports S4 generics as necessary, as the extensions
manual said it does. The manual has also been updated to be a
little more informative on this point.
It is now required that there is an S4 generic (imported or created in the package) when methods are to be exported.
Reference methods cannot safely use non-exported entries in the namespace. We now do not do so, and warn in the documentation.
The namespace import code was warning when identical S4 generic functions were imported more than once, but should not (reported by Brian Ripley, then Martin Morgan).
merge() is no longer allowed (in some ways) to create
a data frame with duplicate column names (which confused
PR#14786).
Fixes for rendering raster images on X11 and Windows devices when the x-axis or y-axis scale is reversed.
getAnywhere() found S3 methods as seen from the
utils namespace and not from the environment from which it
was called.
selectMethod(f, sig) would not return inherited group
methods when caching was off (as it is by default).
dev.copy2pdf(out.type = "cairo") gave an error.
(PR#14827)
Virtual classes (e.g., class unions) had a NULL
prototype even if that was not a legal subclass. See
?setClassUnion.
The C prototypes for zdotc and zdotu in
‘R_ext/BLAS.h’ have been changed to the more modern style
rather than that used by f2c. (Patch by Berwin Turlach.)
isGeneric() produced an error for primitives that
can not have methods.
.C() or .Fortran() had a lack-of-protection
error if the registration information resulted in an argument
being coerced to another type.
boxplot(x=x, at=at) with non finite elements in x
and non integer at could not generate a warning but failed.
heatmap(x, symm=TRUE, RowSideColors=*) no longer
draws the colors in reversed order.
predict(<ar>) was incorrect in the multivariate case,
for p >= 2.
print(x, max=m) is now consistent when x is a
"Date"; also the “reached ... max.print ..” messages
are now consistently using single brackets.
Closed the <li> tag in pages generated by
Rd2HTML(). (PR#14841)
Axis tick marks could go out of range when a log scale was used. (PR#14833)
Signature objects in methods were not allocated as S4
objects (caused a problem with trace() reported by Martin Morgan).
CHANGES IN R VERSION 2.14.2 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.
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.
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.
The included version of zlib has been updated to 1.2.6.
For consistency with the logLik() method,
nobs() for "nls" files now excludes observations
with zero weight. (Reported by Berwin Turlach.)
R CMD check now reports by default on licenses not
according to the description in ‘Writing R Extensions’.
R CMD check has a new option --as-cran to
turn on most of the customizations that CRAN uses for its incoming
checks.
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.
R configured with --disable-openmp would mistakenly
set HAVE_OPENMP (internal) and SUPPORT_OPENMP (in
‘Rconfig.h’) even though no OpenMP flags were populated.
The getS3method() implementation had an old
computation to find an S4 default method.
readLines() could overflow a buffer if the last line
of the file was not terminated. (PR#14766)
R CMD check could miss undocumented S4 objects in
packages which used S4 classes but did not Depends: methods
in their ‘DESCRIPTION’ file.
The HTML Help Search page had malformed links. (PR#14769)
A couple of instances of lack of protection of SEXPs
have been squashed. (PR#14772, PR#14773)
image(x, useRaster=TRUE) misbehaved on single-column
x. (PR#14774)
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)
The text of a function body containing more than 4096 bytes was not properly saved by the parser when entered at the console.
Forgetting the #endif tag in an Rd file could cause
the parser to go into a loop. (Reported by Hans-Jorg Bibiko.)
str(*, ....., strict.width="cut") now also obeys
list.len = n. (Reported by Sören Vogel.)
Printing of arrays did not have enough protection (C level),
e.g., in the context of capture.output(). (Reported by
Hervé Pagès and Martin Morgan.)
pdf(file = NULL) would produce a spurious file named
‘NA’. (PR#14808)
list2env() did not check the type of its envir
argument. (PR#14807)
svg() could segfault if called with a non-existent
file path. (PR#14790)
make install can install to a path containing
+ characters. (PR#14798)
The edit() function did not respect the
options("keep.source") setting. (Reported by Cleridy
Lennert.)
predict.lm(*, type="terms", terms=*, se.fit=TRUE) did
not work. (PR#14817)
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).
The C function R_ReplDLLdo1() did not call top-level
handlers.
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.
mclapply() would fail in code assembling the translated
error message if some (but not all) cores encountered an error.
format.POSIXlt(x) raised an arithmetic exception when
x was an invalid object of class "POSIXlt" and parts
were empty.
installed.packages() has some more protection against
package installs going on in parallel.
.Primitive() could be mis-used to call
.Internal() entry points.
CHANGES IN R VERSION 2.14.1parallel::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.
Reference classes now keep a record of which fields are
locked. $lock() with no arguments returns the names
of the locked fields.
HoltWinters() reports a warning rather than an error
for some optimization failures (where the answer might be a
reasonable one).
tools::dependsOnPkg() now accepts the shorthand
dependencies = "all".
parallel::clusterExport() now allows specification of
an environment from which to export.
The quartz() device now does tilde expansion on its
file argument.
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.
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()).
filled.contour() now accepts infinite values:
previously it might have generated invalid graphics files
(e.g. containing NaN values).
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.
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).
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).
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 ....
stack() now gives an error if no vector column is
selected, rather than returning a 1-column data frame (contrary to
its documentation).
summary.mlm() did not handle objects where the
formula had been specified by an expression. (Reported by
Helios de Rosario Martinez).
tools::deparseLatex(dropBraces=TRUE) could drop
text as well as braces.
colormodel = "grey" (new in R 2.14.0))
did not always work in postscript() and pdf().
file.append() could return TRUE for failures.
(PR#14727)
gzcon() connections are no longer subject to garbage
collection: it was possible for this to happen when unintended
(e.g. when calling load()).
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.)
options(warn = 0) failed to end a (C-level) context
with more than 50 accumulated warnings. (Spotted by Jeffrey
Horner.)
The internal plot.default() code did not do sanity
checks on a cex argument, so invalid input could cause
problems. (Reported by Ben Bolker.)
anyDuplicated(<array>, MARGIN=0) no longer fails.
(Reported by Hervé Pagès.)
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’.
There was a sign error in part of the calculations for the
variance returned by KalmanSmooth(). (PR#14738)
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)
RweaveLatex() now emulates auto-printing rather than
printing, by calling methods::show() when auto-printing
would.
duplicated() ignored fromLast for a
one-column data frame. (PR#14742)
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)
srcfilecopy() has gained a new argument isFile
and now records the working directory, to allow debuggers to find
the original source file. (PR#14826)
LaTeX conversion of Rd files did not correctly handle preformatted backslashes. (PR#14751)
HTML conversion of Rd files did not handle markup within tabular cells properly. (PR#14708)
source() on an empty file with keep.source =
TRUE tried to read from stdin(), in R 2.14.0 only.
(PR#14753)
The code to check Rd files in packages would abort if duplicate description sections were present.
CHANGES IN R VERSION 2.14.0All 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).
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.
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.
:: 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).
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).
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’.
axTicks(*, log=TRUE) has changed in some cases to
satisfy the documented behavior and be consistent.
txtProgressBar() can write to an open connection
instead of the console.
Non-portable package names ending in ‘.’ are no longer allowed. Nor are single-character package names (R was already disallowed).
regexpr() and gregexpr() with perl =
TRUE allows Python-style named captures. (Wish and
contribution of PR#14518.)
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.)
sunflowerplot() now has a formula interface.
(Wish of PR#14541.)
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.
Garbage-collecting an unused input text connection no longer gives a warning (since it ‘connects’ to nothing outside R).
read.table() and scan() have gained a
text argument, to allow reading data from a (possibly
literal) character string.
optim(*, method = .) now allows method = "Brent"
as an interface to optimize(), for use in cases such as
mle() where optim() is used internally.
mosaicplot() gains a border argument.
(Wish of PR#14550.)
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.)
gl() runs faster by avoiding calling factor().
The print() method for object.size() accepts
B as well as b as an abbreviation for ‘bytes’.
unlink() gains a force argument to work like
rm -f and if possible override restrictive permissions.
pbirthday() and qbirthday() now use exact
calculations for coincident = 2.
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.
update.packages() now accepts a character vector of
package names for the oldPkgs argument. (Suggestion of
Tal Galili.)
The special reference class fields .self and
.refClassDef are now read-only to prevent corrupting
the object.
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.)
Rao's efficient score test has been implemented for
glm objects. Specifically, the add1, drop1,
and anova methods now allow test = "Rao".
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.
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.
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.
The default methods for is.finite(), is.infinite()
and is.nan() now signal an error if their argument is not
an atomic vector.
The formula method for plot() no longer places
package stats on the search path (it loads the namespace
instead).
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().
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).
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.
Both curve() and the plot() method for
functions have a new argument xname to facilitate plots
such as sin(t) vs t.
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.
vcov() gains methods for classes "summary.lm" and
"summary.glm".
The plot() method for class "profile.nls"
gains ylab and lty arguments, and passes
... on to plot.default.
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.
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).
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).
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.
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.)
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.)
Sys.info() gains a euser component to report
the ‘effective’ user on OSes which have that concept.
The result returned by try() now contains the
original error condition object as the "condition"
attribute.
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.
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().
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.
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)
There is a new function texi2pdf() in package
tools, currently a convenience wrapper for
texi2dvi(pdf = TRUE).
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’.
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.
tools::Rdiff (by default) and R CMD Rdiff
now ignore differences in pointer values when comparing printed
environments, compiled byte code, etc.
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).
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.
Documentation and messages have been standardized to use “namespace” rather than “name space”.
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.)
Setting the environment variable _R_WARN_ON_LOCKED_BINDINGS_ will give a warning if an attempt is made to change a locked binding.
\SweaveInput is now supported when generating
concordances in Sweave().
findLineNum() and setBreakpoint() now allow
the environment to be specified indirectly; the latter gains
a clear argument to allow it to call untrace().
The body of a closure can be one of further types of R objects, including environments and external pointers.
The Rd2HTML() function in package tools now has
a stylesheet argument, allowing pages to be displayed in
alternate formats.
New function requireNamespace() analogous to
require(), returning a logical value after attempting to
load a namespace.
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.
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.
socketConnection() now has a timeout argument.
It is now documented that large values (package snow used a
year) do not work on some OSes.
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).
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).
New function psnice() in the tools package to
return or change the ‘niceness’ of a process. (Refers to
the ‘priority class’ on Windows.)
list.dirs() gains a recursive argument.
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.
New utility getElement() for accessing either a list
component or a slot in an S4 object.
stars() gains a col.lines argument, thanks to
Dustin Sallings. (Wish of PR#14657.)
New function regmatches() for extracting or replacing
matched or non-matched substrings from match data obtained by
regexpr(), gregexpr() and regexec().
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.)
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.
read.dcf() and write.dcf() gain a
keep.white argument to indicate fields where whitespace
should be kept as is.
available.packages() now works around servers that
fail to return an error code when ‘PACKAGES.gz’ does not
exist. (Patch submitted by Seth Schommer.)
readBin() can now read more than
2^31 - 1 bytes in a single call (the previously
documented limitation).
New function regexec() for finding the positions of
matches as well as all substrings corresponding to parenthesized
subexpressions of the given regular expression.
New function adist() in package utils for
computing ‘edit’ (generalized Levenshtein) distances between
strings.
Class "raster" gains an is.na method to avoid
confusion from the misuse of the matrix method (such as PR#14618).
The identical() function gains an
ignore.bytecode argument to control comparison of
compiled functions.
pmin and pmax now warn if an argument is
partially recycled (wish of PR#14638).
The default for image(useRaster=) is now taken from
option "preferRaster": for the small print see ?image.
str() now displays reference class objects and their
fields, rather than treating them as classical S4 classes.
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.
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".
interaction.plot(*, type = .) now also allows type
"o" or "c".
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.
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.
The pdf() device makes use of Flate compression: this
is controlled by the new logical argument compress, and is
enabled by default.
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).
The bmp(), jpeg(), png() and tiff()
devices now make use of the antialias argument for
type = "quartz".
There are several new built-in font mappings for
X11(type = "Xlib"): see the help on X11Fonts().
There is a new type X11(type = "dbcairo") which
updates the screen less frequently: see its help page.
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.)
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).
New function dev.capture() for capture of bitmap
snapshots of image-based devices (a superset of the functionality
provided by grid.cap() in grid).
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).
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).
The postscript() device only includes the definition
of the sRGB colorspace in the output file for the colormodels
which use it.
The postscript() and pdf() devices now output
greyscale raster images (and not RGB) when colormodel = "gray".
postscript(colormodel = "gray") now accepts non-grey
colours and uses their luminance (as pdf() long has).
colormodel = "grey" is allowed as an alternative name
for postscript() and pdf().
pdf() in the default sRGB colorspace outputs many
fewer changes of colorspace, which may speed up rendering in some
viewing applications.
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.
For pdf(), maxRasters is increased as needed
so the argument is no longer used.
Options keep.source = TRUE, figs.only = FALSE
are now the default.
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.
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).
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’.
R CMD Sweave now supports a --driver
option to select the Sweave driver: the default is equivalent to
--driver=RweaveLatex.
R CMD Sweave and R CMD Stangle support
options --encoding and --options.
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
There is a new option pdf.compress controlling
whether PDF figures are generated using Flate compression (they
are by default).
R CMD Sweave now has a --pdf option to
produce a PDF version of the processed Sweave document.
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.)
Function R_tmpnam2 has been added to the API to allow
a temporary filename to include a specified extension.
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.
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.
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).
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.)
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.
installed.packages() now hashes the names of its
cache files to avoid very rare problems with excessively long path
names. (PR#14669)
A top-level ‘COPYING’ file in a package is no longer installed (file names ‘LICENSE’ or ‘LICENCE’ having long been preferred).
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.
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.
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.
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.
R CMD check now uses a pdf() device when
checking examples (rather than postscript()).
R CMD check now checks line-endings of makefiles
and C/C++/Fortran sources in subdirectories of ‘src’ as well
as in ‘src’ itself.
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).
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).
Reference output for a vignette can be supplied when
checking a package by R CMD check: see ‘Writing R
Extensions’.
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.)
Rscript on a Unix-alike now accepts file names
containing spaces (provided these are escaped or quoted in the
shell).
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.)
require() no longer has a save argument.
The gamma argument to hsv(),
rainbow(), and rgb2hsv() has been removed.
The --no-docs option for
R CMD build --binary is defunct: use
--install-args instead.
The option --unsafe to R CMD INSTALL is
defunct: use the identical option --no-lock instead.
The entry point pythag formerly in ‘Rmath.h’ is
defunct: use instead the C99 function hypot.
R CMD build --binary is formally defunct:
R CMD INSTALL --build has long been the preferred
alternative.
zip.file.extract() is now defunct: use
unzip() or unz() instead.
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.
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.
Forms like binomial(link = "link") for GLM families
deprecated since R 2.4.0 are now defunct.
The declarativeOnly argument to
loadNamespace() (not relevant since R 2.13.0) has been
removed.
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.
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).
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.
Using a false value for the ‘DESCRIPTION’ field LazyLoad is deprecated.
The base and recommended packages are now byte-compiled
(equivalent to make bytecode in R 2.13.x).
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.
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.)
The ‘.afm’ files in package grDevices are now installed as compressed files (as long done on Windows), saving ca 2MB on the installed size.
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.)
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.)
The system call times is required.
The C99 functions acosh, asinh, atanh,
snprintf and vsnprintf are now required.
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.)
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.
Framework installation now supports DESTDIR
(Mac OS X only).
Java detection (R CMD javareconf) works around bogus
java.library.path property in recent Oracle Java binaries.
The locale category LC_MONETARY was only being set on startup on Windows: that is now done on Unix-alikes where supported.
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.
The formula methods for lines(), points() and
text() now work even if package stats is not on the
search path.
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.
Work around an issue in Linux (a system select call
resetting tv) which prevented internet operations from
timing out properly.
Several stack trampling and overflow issues have been fixed
in TRE, triggered by agrep and friends with long patterns.
(PR#14627)
(“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.
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.
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.)
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.
The X11() device's cairo back-end produced incorrect
capture snapshot images on big-endian machines.
loglin() gave a spurious error when argument
margin consisted of a single element of length one.
(PR#14690)
loess() is better protected against misuse,
e.g. zero-length span. (PR#14691)
HoltWinters() checks that the optimization
succeeded. (PR#14694)
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.
round(x, -Inf) now does something sensible (return
zero rather than NA).
signif(x, -Inf) now behaves as documented
(signif(x, 1)) rather than giving zero.
The "table" method for Axis() hardcoded
side = 1, hence calls to plot(<vector>, <table>)
labelled the wrong axis. (PR#14699)
Creating a connection might fail under gctorture(TRUE).
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.
On some systems help(".C", help_type = "pdf") and
similar generated file names that TeX was unable to handle.
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.
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.
A late change in R 2.13.2 broke \Sexpr expressions in Rd files.
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.
qgamma() for small shape underflows to
0 rather than sometimes giving NaN.
(PR#8528, PR#14710)
mapply() now gives an explicit error message (rather
than an obscure one) if inputs of zero and positive length are
mixed.
Setting a Hershey font family followed by string height query would crash R.
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 2.13.2mem.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.
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.)
untar2() now works around errors generated with
tar files that use more than the standard 6 digits for the
checksum. (PR#14654)
install.packages() with Ncpus > 1 guards
against simultaneous installation of indirect dependencies as well
as direct ones.
Sweave now knows about a few more Windows' encodings
(including cp1250 and cp1257) and some
inputenx encodings such as koi8-r.
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".
The default for pdf(maxRasters=) has been increased
from 64 to 1000.
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.
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.
It is possible to build in ‘src/extra/xdr’ on more platforms. (Needed since glibc 2.14 hides its RPC implementation.)
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’.
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.
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).
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.
Build-time expressions in help files did not have access
to functions in the package being built (with R CMD build).
Because quote() did not mark its result as being in
use, modification of the result could in some circumstances
modify the original call.
Plotting pch = '.' now guarantees at least a one-pixel
dot if cex > 0.
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.)
The HTML generated by Rd2HTML() comes closer to
being standards compliant.
filter(x, recursive = TRUE) gave incorrect results on a
series containing NAs. (Spotted by Bill Dunlap.)
Profiling stats::mle() fits with a fixed
parameter was not supported. (PR#14646)
retracemem() was still using positional matching.
(PR#14650)
The quantile method for "ecdf" objects now
works and is documented.
xtabs(~ .., ..., sparse=TRUE) now also works together
with an exclude = .. specification.
decompose() computed an incorrect seasonal component for
time series with odd frequencies.
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.
.hasSlot() wrongly gave FALSE in some cases.
Sweave() with keep.source=TRUE could generate
spurious NA lines when a chunk reference appeared last in
a code chunk.
\Sexpr[results=rd] in an ‘.Rd’ file now first tries
parse_Rd(fragment=FALSE) to allow Rd section-level macros
to be inserted.
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)
In rare cases ks.test() could return a p-value
very slightly less than 0 by rounding error. (PR#14671)
If trunc() was called on a "POSIXlt" vector
and the result was subsetted, all but the first element was
converted to NA. (PR#14679)
cbind() and rbind() could cause memory
corruption when used on a combination of raw and logical/integer
vectors.
CHANGES IN R VERSION 2.13.1iconv() no longer translates NA strings as
"NA".
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)
RShowDoc() can now display the licences shipped with
R, e.g. RShowDoc("GPL-3").
New wrapper function showNonASCIIfile() in package
tools.
nobs() now has a "mle" method in package
stats4.
trace() now deals correctly with S4 reference classes
and corresponding reference methods (e.g., $trace())
have been added.
xz has been updated to 5.0.3 (very minor bugfix
release).
tools::compactPDF() gets more compression (usually a
little, sometimes a lot) by using the compressed object streams of
PDF 1.5.
cairo_ps(onefile = TRUE) generates encapsulated EPS
on platforms with cairo >= 1.6.
Binary reads (e.g. by readChar() and readBin())
are now supported on clipboard connections. (Wish of PR#14593.)
as.POSIXlt.factor() now passes ... to the
character method (suggestion of Joshua Ulrich). [Intended for R
2.13.0 but accidentally removed before release.]
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).
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.
make install-strip failed under some configuration
options.
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() 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.
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.
Sweave custom graphics devices can have a custom function
foo.off() to shut them down.
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).
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).
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.
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.
The internal functions .readRDS() and
.saveRDS() are now deprecated in favour of the public
functions readRDS() and saveRDS() introduced in R
2.13.0.
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.
The off-line help() types "postscript" and
"ps" are deprecated.
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.
R CMD build now looks for ‘DESCRIPTION’
fields BuildResaveData and BuildKeepEmpty for
per-package overrides. See ‘Writing R Extensions’.
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)
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.)
dataframe[[row,col]] now dispatches on [[
methods for the selected column. (Spotted by Bill Dunlap).
sort.int() would strip the class of an object, but
leave its object bit set. (Reported by Bill Dunlap.)
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’)
Complex arithmetic sometimes warned incorrectly about producing NAs when there were NaNs in the input.
seek(origin = "current") incorrectly reported it was
not implemented for a gzfile() connection.
c(), unlist(), cbind() and
rbind() could silently overflow the maximum vector length
and cause a segfault. (PR#14571)
The fonts argument to X11(type = "Xlib") was
being ignored.
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.)
Parsed text containing embedded newlines was printed
incorrectly by as.character.srcref(). (Reported by Hadley
Wickham.)
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.)
fields = list() failed for setRefClass().
(Reported by Michael Lawrence.)
Reference classes could not redefine an inherited field
which had class "ANY". (Reported by Janko Thyson.)
Methods that override previously loaded versions will now be installed and called. (Reported by Iago Mosqueira.)
addmargins() called numeric(apos) rather than
numeric(length(apos)).
The HTML help search sometimes produced bad links. (PR#14608)
Command completion will no longer be broken if
tail.default() is redefined by the user. (Problem reported
by Henrik Bengtsson.)
LaTeX rendering of markup in titles of help pages has been
improved; in particular, \eqn{} may be used there.
isClass() used its own namespace as the default of
the where argument inadvertently.
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.)
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 2.13.0replicate() (by default) and vapply() (always)
now return a higher-dimensional array instead of a matrix in the case
where the inner function value is an array of dimension >= 2.
Printing and formatting of floating point numbers is now using the correct number of digits, where it previously rarely differed by a few digits. (See “scientific” entry below.) This affects many ‘*.Rout.save’ checks in packages.
normalizePath() has been moved to the base
package (from utils): this is so it can be used by
library() and friends.
It now does tilde expansion.
It gains new arguments winslash (to select the separator on
Windows) and mustWork to control the action if a canonical
path cannot be found.
The previously barely documented limit of 256 bytes on a
symbol name has been raised to 10,000 bytes (a sanity check).
Long symbol names can sometimes occur when deparsing expressions
(for example, in model.frame).
reformulate() gains a intercept argument.
cmdscale(add = FALSE) now uses the more common
definition that there is a representation in n-1 or less
dimensions, and only dimensions corresponding to positive
eigenvalues are used. (Avoids confusion such as PR#14397.)
Names used by c(), unlist(), cbind()
and rbind() are marked with an encoding when this can be
ascertained.
R colours are now defined to refer to the sRGB color space.
The PDF, PostScript, and Quartz graphics devices record this fact. X11 (and cairo) and Windows just assume that your screen conforms.
system.file() gains a mustWork argument
(suggestion of Bill Dunlap).
new.env(hash = TRUE) is now the default.
list2env(envir = NULL) defaults to hashing (with a
suitably sized environment) for lists of more than 100 elements.
text() gains a formula method.
IQR() now has a type argument which is passed
to quantile().
as.vector(), as.double() etc duplicate less
when they leave the mode unchanged but remove attributes.
as.vector(mode = "any") no longer duplicates when it does
not remove attributes. This helps memory usage in matrix()
and array().
matrix() duplicates less if data is an atomic vector
with attributes such as names (but no class).
dim(x) <- NULL duplicates less if x has neither
dimensions nor names (since this operation removes names and
dimnames).
setRepositories() gains an addURLs argument.
chisq.test() now also returns a stdres
component, for standardized residuals (which have unit variance,
unlike the Pearson residuals).
write.table() and friends gain a fileEncoding
argument, to simplify writing files for use on other OSes (e.g. a
spreadsheet intended for Windows or Mac OS X Excel).
Assignment expressions of the form foo::bar(x) <- y
and foo:::bar(x) <- y now work; the replacement functions
used are foo::`bar<-` and foo:::`bar<-`.
Sys.getenv() gains a names argument so
Sys.getenv(x, names = FALSE) can replace the common idiom
of as.vector(Sys.getenv()). The default has been changed
to not name a length-one result.
Lazy loading of environments now preserves attributes and locked status. (The locked status of bindings and active bindings are still not preserved; this may be addressed in the future).
options("install.lock") may be set to FALSE
so that install.packages() defaults to --no-lock
installs, or (on Windows) to TRUE so that binary installs
implement locking.
sort(partial = p) for large p now tries
Shellsort if quicksort is not appropriate and so works for
non-numeric atomic vectors.
sapply() gets a new option simplify = "array"
which returns a “higher rank” array instead of just a matrix
when FUN() returns a dim() length of two or more.
replicate() has this option set by default, and
vapply() now behaves that way internally.
aperm() becomes S3 generic and gets a table
method which preserves the class.
merge() and as.hclust() methods for objects of
class "dendrogram" are now provided.
The character method of as.POSIXlt() now tries to
find a format that works for all non-NA inputs, not just
the first one.
str() now has a method for class "Date"
analogous to that for class "POSIXt".
New function file.link() to create hard links on
those file systems (POSIX, NTFS but not FAT) that support them.
New Summary() group method for class "ordered"
implements min(), max() and range() for
ordered factors.
mostattributes<-() now consults the "dim"
attribute and not the dim() function, making it more useful
for objects (such as data frames) from classes with methods for
dim(). It also uses attr<-() in preference to the
generics name<-(), dim<-() and dimnames<-().
(Related to PR#14469.)
There is a new option "browserNLdisabled" to disable
the use of an empty (e.g. via the ‘Return’ key) as a synonym
for c in browser() or n under debug().
(Wish of PR#14472.)
example() gains optional new arguments
character.only and give.lines enabling programmatic
exploration.
serialize() and unserialize() are no longer
described as ‘experimental’. The interface is now regarded
as stable, although the serialization format may well change in
future releases. (serialize() has a new argument
version which would allow the current format to be written
if that happens.)
New functions saveRDS() and readRDS() are public
versions of the ‘internal’ functions .saveRDS() and
.readRDS() made available for general use. The dot-name
versions remain available as several package authors have made use
of them, despite the documentation. readRDS() no longer
wraps non-file connections in a call to gzcon(), for
efficiency (see its documentation).
saveRDS() supports compress = "xz".
Many functions when called with a not-open connection will
now ensure that the connection is left not-open in the event of
error. These include read.dcf(), dput(),
dump(), load(), parse(), readBin(),
readChar(), readLines(), save(),
writeBin(), writeChar(), writeLines(),
.readRDS(), .saveRDS() and tools::parse_Rd(),
as well as functions calling these.
Public functions find.package() and path.package()
replace the internal dot-name versions.
The default method for terms() now looks for a
"terms" attribute if it does not find a "terms"
component, and so works for model frames.
httpd() handlers receive an additional argument
containing the full request headers as a raw vector (this can be
used to parse cookies, multi-part forms etc.). The recommended
full signature for handlers is therefore function(url,
query, body, headers, ...).
file.edit() gains a fileEncoding argument to
specify the encoding of the file(s).
The format of the HTML package listings has changed. If there is more than one library tree , a table of links to libraries is provided at the top and bottom of the page. Where a library contains more than 100 packages, an alphabetic index is given at the top of the section for that library. (As a consequence, package names are now sorted case-insensitively whatever the locale.)
isSeekable() now returns FALSE on connections
which have non-default encoding. Although documented to
record if ‘in principle’ the connection supports seeking,
it seems safer to report FALSE when it may not work.
R CMD REMOVE and remove.packages() now
remove file R.css when removing all remaining packages in a
library tree. (Related to the wish of PR#14475: note that this
file is no longer installed.)
unzip() now has a unzip argument like
zip.file.extract(). This allows an external
unzip program to be used, which can be useful to access
features supported by Info-ZIP's unzip version 6 which
is now becoming more widely available.
There is a simple zip() function, as wrapper for an
external zip command.
bzfile() connections can now read from concatenated
bzip2 files (including files written with
bzfile(open = "a")) and files created by some other
compressors (such as the example of PR#14479).
The primitive function c() is now of type BUILTIN.
plot(<dendrogram>, .., nodePar=*) now obeys an optional
xpd specification (allowing clipping to be turned off
completely).
nls(algorithm="port") now shares more code with
nlminb(), and is more consistent with the other
nls() algorithms in its return value.
xz has been updated to 5.0.1 (very minor bugfix
release).
image() has gained a logical useRaster
argument allowing it to use a bitmap raster for plotting a
regular grid instead of polygons. This can be more efficient, but
may not be supported by all devices. The default is FALSE.
list.files()/dir() gains a new argument
include.dirs() to include directories in the listing when
recursive = TRUE.
New function list.dirs() lists all directories,
(even empty ones).
file.copy() now (by default) copies
read/write/execute permissions on files, moderated by the current
setting of Sys.umask().
Sys.umask() now accepts mode = NA and returns
the current umask value (visibly) without changing it.
There is a ! method for classes "octmode" and
"hexmode": this allows xor(a, b) to work if both
a and b are from one of those classes.
as.raster() no longer fails for vectors or matrices
containing NAs.
New hook "before.new.plot" allows functions to be run
just before advancing the frame in plot.new, which is
potentially useful for custom figure layout implementations.
Package tools has a new function compactPDF()
to try to reduce the size of PDF files via qpdf
or gs.
tar() has a new argument extra_flags.
dotchart() accepts more general objects x such
as 1D tables which can be coerced by as.numeric() to a
numeric vector, with a warning since that might not be
appropriate.
The previously internal function create.post() is now
exported from utils, and the documentation for
bug.report() and help.request() now refer to that
for create.post().
It has a new method = "mailto" on Unix-alikes similar to
that on Windows: it invokes a default mailer via open
(Mac OS X) or xdg-open or the default browser (elsewhere).
The default for ccaddress is now
getOption("ccaddress") which is by default unset: using the
username as a mailing address nowadays rarely works as expected.
The default for options("mailer") is now
"mailto" on all platforms.
unlink() now does tilde-expansion (like most other
file functions).
file.rename() now allows vector arguments (of the
same length).
The "glm" method for logLik() now returns an
"nobs" attribute (which stats4::BIC() assumed it
did).
The "nls" method for logLik() gave incorrect results
for zero weights.
There is a new generic function nobs() in package
stats, to extract from model objects a suitable value for
use in BIC calculations. An S4 generic derived from it is defined
in package stats4.
Code for S4 reference-class methods is now examined for possible errors in non-local assignments.
findClasses, getGeneric, findMethods
and hasMethods are revised to deal consistently with
the package= argument and be consistent with soft namespace
policy for finding objects.
tools::Rdiff() now has the option to return not only
the status but a character vector of observed differences (which
are still by default sent to ‘stdout’).
The startup environment variables R_ENVIRON_USER, R_ENVIRON, R_PROFILE_USER and R_PROFILE are now treated more consistently. In all cases an empty value is considered to be set and will stop the default being used, and for the last two tilde expansion is performed on the file name. (Note that setting an empty value is probably impossible on Windows.)
Using R --no-environ CMD, R
--no-site-file CMD or R --no-init-file CMD sets
environment variables so these settings are passed on to child R
processes, notably those run by INSTALL, check and
build. R --vanilla CMD sets these three options
(but not --no-restore).
smooth.spline() is somewhat faster. With
cv=NA it allows some leverage computations to be skipped,
The internal (C) function scientific(), at the heart
of 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.
A new function grepRaw() has been introduced for
finding subsets of raw vectors. It supports both literal searches
and regular expressions.
Package compiler is now provided as a standard
package. See ?compiler::compile for information on how to
use the compiler. This package implements a byte code compiler
for R: by default the compiler is not used in this release. See
the ‘R Installation and Administration Manual’ for how to
compile the base and recommended packages.
Providing an exportPattern directive in a NAMESPACE
file now causes classes to be exported according to the same
pattern, for example the default from package.skeleton()
to specify all names starting with a letter. An explicit
directive to exportClassPattern will still over-ride.
There is an additional marked encoding "bytes" for
character strings. This is intended to be used for non-ASCII
strings which should be treated as a set of bytes, and never
re-encoded as if they were in the encoding of the 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.
The new function removeSource() removes the internally
stored source from a function.
"srcref" attributes now include two additional
line number values, recording the line numbers in the order they
were parsed.
New functions have been added for source reference access:
getSrcFilename(), getSrcDirectory(),
getSrcLocation() and getSrcref().
Sys.chmod() has an extra argument use_umask
which defaults to true and restricts the file mode by the current
setting of umask. This means that all the R functions
which manipulate file/directory permissions by default respect
umask, notably R CMD INSTALL.
tempfile() has an extra argument fileext to
create a temporary filename with a specified extension.
(Suggestion and initial implementation by Dirk Eddelbuettel.)
There are improvements in the way Sweave() and
Stangle() handle non-ASCII vignette sources, especially in
a UTF-8 locale: see ‘Writing R Extensions’ which now has a
subsection on this topic.
factanal() now returns the rotation matrix if a
rotation such as "promax" is used, and hence factor
correlations are displayed. (Wish of PR#12754.)
The gctorture2() function provides a more refined
interface to the GC torture process. Environment variables
R_GCTORTURE, R_GCTORTURE_WAIT, and
R_GCTORTURE_INHIBIT_RELEASE can also be used to control the
GC torture process.
file.copy(from, to) no longer regards it as an error
to supply a zero-length from: it now simply does nothing.
rstandard.glm() gains a type argument which can
be used to request standardized Pearson residuals.
A start on a Turkish translation, thanks to Murat Alkan.
.libPaths() calls normalizePath(winslash = "/")
on the paths: this helps (usually) to present them in a
user-friendly form and should detect duplicate paths accessed via
different symbolic links.
download.file() can be now used with external methods
even if there are spaces in the URL or the target filename.
The first formal argument of .C(), .Fortran(),
.Call() and .External() is now referred to a
.NAME rather than name: however actual calls should
have an unnamed first argument.
Sweave() has options to produce PNG and JPEG figures,
and to use a custom function to open a graphics device (see
?RweaveLatex).
(Based in part on the contribution of PR#14418.)
The default for Sweave() is to produce only PDF
figures (rather than both EPS and PDF).
Environment variable SWEAVE_OPTIONS can be used to supply defaults for existing or new options to be applied after the Sweave driver setup has been run.
The Sweave manual is now included as a vignette in the utils package.
Sweave() handles keep.source=TRUE much better:
it could duplicate some lines and omit comments. (Reported by John
Maindonald and others.)
Because they use a C99 interface which a C++ compiler is not
required to support, Rvprintf and REvprintf are only
defined by ‘R_ext/Print.h’ in C++ code if the macro
R_USE_C99_IN_CXX is defined when it is included.
pythag duplicated the C99 function hypot. It
is no longer provided, but is used as a substitute for hypot
in the very unlikely event that the latter is not available.
R_inspect(obj) and R_inspect3(obj, deep, pvec)
are (hidden) C-level entry points to the internal inspect
function and can be used for C-level debugging (e.g., in conjunction
with the p command in gdb).
Compiling R with --enable-strict-barrier now also
enables additional checking for use of unprotected objects. In
combination with gctorture() or gctorture2() and a
C-level debugger this can be useful for tracking down memory
protection issues.
R CMD Rdiff is now implemented in R on
Unix-alikes (as it has been on Windows since R 2.12.0).
R CMD build no longer does any cleaning in the
supplied package directory: all the cleaning is done in the copy.
It has a new option --install-args to pass arguments to
R CMD INSTALL for --build (but not when
installing to rebuild vignettes).
There is new option, --resave-data, to call
tools::resaveRdaFiles() on the ‘data’ directory, to
compress tabular files (‘.tab’, ‘.csv’ etc) and to
convert ‘.R’ files to ‘.rda’ files. The default,
--resave-data=gzip, is to do so in a way compatible even
with years-old versions of R, but better compression is given by
--resave-data=best, requiring R >= 2.10.0.
It now adds a ‘datalist’ file for ‘data’ directories of more than 1Mb.
Patterns in ‘.Rbuildignore’ are now also matched against all directory names (including those of empty directories).
There is a new option, --compact-vignettes, to try
reducing the size of PDF files in the ‘inst/doc’ directory.
Currently this tries qpdf: other options may be used in
future.
When re-building vignettes and a ‘inst/doc/Makefile’ file is
found, make clean is run if the makefile has a
clean: target.
After re-building vignettes the default clean-up operation will remove any directories (and not just files) created during the process: e.g. one package created a ‘.R_cache’ directory.
Empty directories are now removed unless the option --keep-empty-dirs is given (and a few packages do deliberately include empty directories).
If there is a field BuildVignettes in the package
‘DESCRIPTION’ file with a false value, re-building the
vignettes is skipped.
R CMD check now also checks for filenames that are
case-insensitive matches to Windows' reserved file names with
extensions, such as ‘nul.Rd’, as these have caused problems
on some Windows systems.
It checks for inefficiently saved ‘data/*.rda’ and ‘data/*.RData’ files, and reports on those large than 100Kb. A more complete check (including of the type of compression, but potentially much slower) can be switched on by setting environment variable _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).
R CMD check now warns if it finds
‘inst/doc/makefile’, and R CMD build renames such a
file to ‘inst/doc/Makefile’.
Installing R no longer tries to find perl, and
R CMD no longer tries to substitute a full path for
awk nor perl – this was a legacy from the
days when they were used by R itself. Because a couple of
packages do use awk, it is set as the make
(rather than environment) variable AWK.
make check will now fail if there are differences
from the reference output when testing package examples and if
environment variable R_STRICT_PACKAGE_CHECK is set to a true
value.
The C99 double complex type is now required.
The C99 complex trigonometric functions (such as csin) are not currently required (FreeBSD lacks most of them): substitutes are used if they are missing.
The C99 system call va_copy is now required.
If environment variable R_LD_LIBRARY_PATH is set during configuration (for example in ‘config.site’) it is used unchanged in file ‘etc/ldpaths’ rather than being appended to.
configure looks for support for OpenMP and if
found compiles R with appropriate flags and also makes them
available for use in packages: see ‘Writing R Extensions’.
This is currently experimental, and is only used in R with a
single thread for colSums() and colMeans(). Expect
it to be more widely used in later versions of R.
This can be disabled by the --disable-openmp flag.
R CMD INSTALL --clean now removes copies of a
‘src’ directory which are created when multiple
sub-architectures are in use. (Following a comment from
Berwin Turlach.)
File ‘R.css’ is now installed on a per-package basis (in the package's ‘html’ directory) rather than in each library tree, and this is used for all the HTML pages in the package. This helps when installing packages with static HTML pages for use on a webserver. It will also allow future versions of R to use different stylesheets for the packages they install.
A top-level file ‘.Rinstignore’ in the package sources
can list (in the same way as ‘.Rbuildignore’) files under
inst that should not be installed. (Why should there be any
such files? Because all the files needed to re-build vignettes
need to be under inst/doc, but they may not need to be
installed.)
R CMD INSTALL has a new option
--compact-docs to compact any PDFs under the
‘inst/doc’ directory. Currently this uses qpdf,
which must be installed (see ‘Writing R Extensions’).
There is a new option --lock which can be used to cancel the effect of --no-lock or --pkglock earlier on the command line.
Option --pkglock can now be used with more than one package, and is now the default if only one package is specified.
Argument lock of install.packages() can now be
use for Mac binary installs as well as for Windows ones. The
value "pkglock" is now accepted, as well as TRUE and
FALSE (the default).
There is a new option --no-clean-on-error for
R CMD INSTALL to retain a partially installed package for
forensic analysis.
Packages with names ending in ‘.’ are not portable
since Windows does not work correctly with such directory names.
This is now warned about in R CMD check, and will not be
allowed in R 2.14.x.
The vignette indices are more comprehensive (in the style of
browseVignetttes()).
require(save = TRUE) is defunct, and use of the
save argument is deprecated.
R CMD check --no-latex is defunct: use
--no-manual instead.
R CMD Sd2Rd is defunct.
The gamma argument to hsv(),
rainbow(), and rgb2hsv() is deprecated
and no longer has any effect.
The previous options for R CMD build --binary
(--auto-zip, --use-zip-data and
--no-docs) are deprecated (or defunct):
use the new option --install-args instead.
When a character value is used for the EXPR
argument in switch(), only a single unnamed alternative
value is now allowed.
The wrapper utils::link.html.help() is no longer
available.
Zip-ing data sets in packages (and hence R CMD
INSTALL options --use-zip-data and --auto-zip, as
well as the ZipData: yes field in a DESCRIPTION file)
is defunct.
Installed packages with zip-ed data sets can still be used, but a warning that they should be re-installed will be given.
The ‘experimental’ alternative specification of a
namespace via .Export() etc is now defunct.
The option --unsafe to R CMD INSTALL is
deprecated: use the identical option --no-lock instead.
The entry point pythag in ‘Rmath.h’ is deprecated
in favour of the C99 function hypot. A wrapper for
hypot is provided for R 2.13.x only.
Direct access to the "source" attribute of functions
is deprecated; use deparse(fn, control="useSource") to access
it, and removeSource(fn) to remove it.
R CMD build --binary is now formally deprecated:
R CMD INSTALL --build has long been the preferred
alternative.
Single-character package names are deprecated (and R is already disallowed to avoid confusion in Depends: fields).
drop.terms and the [ method for class
"terms" no longer add back an intercept. (Reported by
Niels Hansen.)
aggregate preserves the class of a column (e.g. a
date) under some circumstances where it discarded the class
previously.
p.adjust() now always returns a vector result, as
documented. In previous versions it copied attributes (such as
dimensions) from the p argument: now it only copies names.
On PDF and PostScript devices, a line width of zero was recorded verbatim and this caused problems for some viewers (a very thin line combined with a non-solid line dash pattern could also cause a problem). On these devices, the line width is now limited at 0.01 and for very thin lines with complex dash patterns the device may force the line dash pattern to be solid. (Reported by Jari Oksanen.)
The str() method for class "POSIXt" now gives
sensible output for 0-length input.
The one- and two-argument complex maths functions failed to warn if NAs were generated (as their numeric analogues do).
Added .requireCachedGenerics to the dont.mind
list for library() to avoid warnings about duplicates.
$<-.data.frame messed with the class attribute,
breaking any S4 subclass. The S4 data.frame class now has its own
$<- method, and turns dispatch on for this primitive.
Map() did not look up a character argument f
in the correct frame, thanks to lazy evaluation. (PR#14495)
file.copy() did not tilde-expand from and to
when to was a directory. (PR#14507)
It was possible (but very rare) for the loading test in
R CMD INSTALL to crash a child R process and so leave
around a lock directory and a partially installed package. That
test is now done in a separate process.
plot(<formula>, data=<matrix>,..) now works in more
cases; similarly for points(), lines() and
text().
edit.default() contained a manual dispatch for matrices
(the "matrix" class didn't really exist when it was written).
This caused an infinite recursion in the no-GUI case and has now
been removed.
data.frame(check.rows = TRUE) sometimes worked when
it should have detected an error. (PR#14530)
scan(sep= , strip.white=TRUE) sometimes stripped
trailing spaces from within quoted strings. (The real bug in
PR#14522.)
The rank-correlation methods for cor() and
cov() with use = "complete.obs" computed the ranks
before removing missing values, whereas the documentation implied
incomplete cases were removed first. (PR#14488)
They also failed for 1-row matrices.
The perpendicular adjustment used in placing text and
expressions in the margins of plots was not scaled by
par("mex"). (Part of PR#14532.)
Quartz Cocoa device now catches any Cocoa exceptions that occur during the creation of the device window to prevent crashes. It also imposes a limit of 144 ft^2 on the area used by a window to catch user errors (unit misinterpretation) early.
The browser (invoked by debug(), browser()
or otherwise) would display attributes such as "wholeSrcref"
that were intended for internal use only.
R's internal filename completion now properly handles
filenames with spaces in them even when the readline library is
used. This resolves PR#14452 provided the internal filename
completion is used (e.g., by setting rc.settings(files =
TRUE)).
Inside uniroot(f, ...), -Inf function values
are now replaced by a maximally negative value.
rowsum() could silently over/underflow on integer
inputs (reported by Bill Dunlap).
as.matrix() did not handle "dist" objects with
zero rows.
CHANGES IN R VERSION 2.12.2 patchedmax() 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.)
A change to the C function R_tryEval had broken error messages in S4 method selection; the error message is now printed.
PDF output with a non-RGB color model used RGB for the line stroke color. (PR#14511)
stats4::BIC() assumed without checking that an object
of class "logLik" has an "nobs" attribute:
glm() fits did not and so BIC() failed for them.
In some circumstances a one-sided mantelhaen.test()
reported the p-value for the wrong tail. (PR#14514)
Passing the invalid value lty = NULL to axis()
sent an invalid value to the graphics device, and might cause the
device to segfault.
Sweave() with concordance=TRUE could lead to
invalid PDF files; ‘Sweave.sty’ has been updated to avoid
this.
Non-ASCII characters in the titles of help pages were not rendered properly in some locales, and could cause errors or warnings.
checkRd() gave a spurious error if the \href
macro was used.
CHANGES IN R VERSION 2.12.2 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).
There is a workaround for crashes seen with several packages on systems using zlib 1.2.5: see the INSTALLATION section.
PCRE has been updated to 8.12 (two bug-fix releases since 8.10).
rep(), seq(), seq.int() and
seq_len() report more often when the first element is taken
of an argument of incorrect length.
The Cocoa back-end for the quartz() graphics device
on Mac OS X provides a way to disable event loop processing
temporarily (useful, e.g., for forked instances of R).
kernel()'s default for m was not appropriate
if coef was a set of coefficients. (Reported by Pierre
Chausse.)
bug.report() has been updated for the current R bug
tracker, which does not accept emailed submissions.
R CMD check now checks for the correct use of
$(LAPACK_LIBS) (as well as $(BLAS_LIBS)), since
several CRAN recent submissions have ignored ‘Writing R
Extensions’.
The zlib sources in the distribution are now built with all symbols remapped: this is intended to avoid problems seen with packages such as XML and rggobi which link to ‘zlib.so.1’ on systems using zlib 1.2.5.
The default for FFLAGS and FCFLAGS with
gfortran on x86_64 Linux has been changed back to -g
-O2: however, setting -g -O may still be needed for
gfortran 4.3.x.
A LazyDataCompression field in the ‘DESCRIPTION’
file will be used to set the value for the
--data-compress option of R CMD INSTALL.
Files ‘R/sysdata.rda’ of more than 1Mb are now stored
in the lazyload database using xz compression: this for
example halves the installed size of package Imap.
R CMD INSTALL now ensures that directories
installed from ‘inst’ have search permission for everyone.
It no longer installs files ‘inst/doc/Rplots.ps’ and
‘inst/doc/Rplots.pdf’. These are almost certainly left-overs
from Sweave runs, and are often large.
The ‘experimental’ alternative specification of a
namespace via .Export() etc is now deprecated.
zip.file.extract() is now deprecated.
Zip-ing data sets in packages (and hence R CMD
INSTALL --use-zip-data and the ZipData: yes field in a
DESCRIPTION file) is deprecated: using efficiently
compressed ‘.rda’ images and lazy-loading of data has
superseded it.
identical() could in rare cases generate a warning
about non-pairlist attributes on CHARSXPs. As these are used for
internal purposes, the attribute check should be skipped.
(Reported by Niels Richard Hansen).
If the filename extension (usually ‘.Rnw’) was not
included in a call to Sweave(), source references would not
work properly and the keep.source option failed. (PR#14459)
format.data.frame() now keeps zero character column names.
pretty(x) no longer raises an error when x
contains solely non-finite values. (PR#14468)
The plot.TukeyHSD() function now uses a line width of
0.5 for its reference lines rather than lwd = 0 (which
caused problems for some PDF and PostScript viewers).
The big.mark argument to prettyNum(),
format(), etc. was inserted reversed if it was more than
one character long.
R CMD check failed to check the filenames under
‘man’ for Windows' reserved names.
The "Date" and "POSIXt" methods for
seq() could overshoot when to was supplied and
by was specified in months or years.
The internal method of untar() now restores hard
links as file copies rather than symbolic links (which did not
work for cross-directory links).
unzip() did not handle zip files which contained
filepaths with two or more leading directories which were not in
the zipfile and did not already exist. (It is unclear if such
zipfiles are valid and the third-party C code used did not support
them, but PR#14462 created one.)
combn(n, m) now behaves more regularly for the border
case m = 0. (PR#14473)
The rendering of numbers in plotmath expressions (e.g.
expression(10^2)) used the current settings for conversion
to strings rather than setting the defaults, and so could be
affected by what has been done before. (PR#14477)
The methods of napredict() and naresid() for
na.action = na.exclude fits did not work correctly in the
very rare event that every case had been omitted in the fit.
(Reported by Simon Wood.)
weighted.residuals(drop0=TRUE) returned a vector when
the residuals were a matrix (e.g. those of class "mlm").
(Reported by Bill Dunlap.)
Package HTML index files ‘<pkg>/html/00Index.html’ were generated with a stylesheet reference that was not correct for static browsing in libraries.
ccf(na.action = na.pass) was not implemented.
The parser accepted some incorrect numeric constants,
e.g. 20x2. (Reported by Olaf Mersmann.)
format(*, zero.print) did not always replace the full
zero parts.
Fixes for subsetting or subassignment of "raster"
objects when not both i and j are specified.
R CMD INSTALL was not always respecting the
ZipData: yes field of a ‘DESCRIPTION’ file (although
this is frequently incorrectly specified for packages with no data
or which specify lazy-loading of data).
R CMD INSTALL --use-zip-data was incorrectly implemented
as --use-zipdata since R 2.9.0.
source(file, echo=TRUE) could fail if the file
contained #line directives. It now recovers more gracefully, but
may still display the wrong line if the directive gives incorrect
information.
atan(1i) returned NaN+Infi (rather than
0+Infi) on platforms without C99 complex support.
library() failed to cache S4 metadata (unlike
loadNamespace()) causing failures in S4-using packages
without a namespace (e.g. those using reference classes).
The function qlogis(lp, log.p=TRUE) no longer
prematurely overflows to Inf when exp(lp) is close to 1.
Updating S4 methods for a group generic function requires resetting the methods tables for the members of the group (patch contributed by Martin Morgan).
In some circumstances (including for package XML),
R CMD INSTALL installed version-control directories from
source packages.
Added PROTECT calls to some constructed expressions
used in C level eval calls.
utils:::create.post() (used by bug.report()
and help.request()) failed to quote arguments to the
mailer, and so often failed.
bug.report() was naive about how to extract
maintainer email addresses from package descriptions, so would
often try mailing to incorrect addresses.
debugger() could fail to read the environment of a
call to a function with a ... argument. (Reported by
Charlie Roosen.)
prettyNum(c(1i, NA), drop0=TRUE) or
str(NA_complex_) now work correctly.
CHANGES IN R VERSION 2.12.1The DVI/PDF reference manual now includes the help pages for all the standard packages: splines, stats4 and tcltk were previously omitted (intentionally).
http://www.rforge.net has been added to the default
set of repositories known to setRepositories().
xz-utils has been updated to version 5.0.0.
reshape() now makes use of sep when forming
names during reshaping to wide format. (PR#14435)
legend() allows the length of lines to be set by the
end user via the new argument seg.len.
New S4 reference class utility methods copy(),
field(), getRefClass() and getClass() have
been added to package methods.
When a character value is used for the EXPR
argument in switch(), a warning is given if more than
one unnamed alternative value is given. This will become an
error in R 2.13.0.
StructTS(type = "BSM") now allows series with just
two seasons. (Reported by Birgit Erni.)
The PDF reference manual is now built as PDF version 1.5 with object compression, which on platforms for which this is not the default (notably MiKTeX) halves its size.
Variable FCLIBS can be set during configuration, for any additional library flags needed when linking a shared object with the Fortran 9x compiler. (Needed with Solaris Studio 12.2.)
seq.int() no longer sometimes evaluates arguments
twice. (PR#14388)
The data.frame method of format() failed if a
column name was longer than 256 bytes (the maximum length allowed
for an R name).
predict(<lm object>, type ="terms", ...) failed if
both terms and interval were specified. (Reported
by Bill Dunlap.)
Also, if se.fit = TRUE the standard errors were reported
for all terms, not just those selected by a non-null terms.
The TRE regular expressions engine could terminate R rather than give an error when given certain invalid regular expressions. (PR#14398)
cmdscale(eig = TRUE) was documented to return n-1
eigenvalues but in fact only returned k. It now returns
all n eigenvalues.
cmdscale(add = TRUE) failed to centre the return
configuration and sometimes lost the labels on the points. Its
return value was described wrongly (it is always a list and
contains component ac).
promptClass() in package methods now works for
reference classes and gives a suitably specialized skeleton of
documentation.
Also, callSuper() now works via the methods()
invocation as well as for initially specified methods.
download.file() could leave the destination file open
if the URL was not able to be opened. (PR#14414)
Assignment of an environment to functions or as an attribute
to other objects now works for S4 subclasses of "environment".
Use of [[<- for S4 subclasses of
"environment" generated an infinite recursion from the
method. The method has been replaced by internal code.
In a reference class S4 method, callSuper() now works in
initialize() methods when there is no explicit superclass
method.
! dropped attributes such as names and dimensions from a length-zero argument. (PR#14424)
When list2env() created an environment it was missing
a PROTECT call and so was vulnerable to garbage collection.
Sweave() with keep.source=TRUE dropped
comments at the start and end of code chunks. It could also
fail when \SweaveInput was combined with named chunks.
The Fortran code used by nls(algorithm = "port")
could infinite-loop when compiled with high optimization on a
modern version of gcc, and SAFE_FFLAGS is now used
to make this less likely. (PR#14427, seen with 32-bit Windows
using gcc 4.5.0 used from R 2.12.0.)
sapply() with default simplify = TRUE and
mapply() with default SIMPLIFY = TRUE wrongly
simplified language-like results, as, e.g., in
mapply(1:2, c(3,7), FUN = function(i,j) call(':',i,j)).
Backreferences to undefined patterns in
[g]sub(pcre = TRUE) could cause a segfault. (PR#14431)
The format() (and hence the print()) method
for class "Date" rounded fractional dates towards zero: it
now always rounds them down.
Reference S4 class creation could generate ambiguous inheritance patterns under very special circumstances.
[[<- turned S4 subclasses of "environment" into
plain environments.
Long titles for help pages were truncated in package indices and a few other places.
Additional utilities now work correctly with S4 subclasses of
"environment" (rm, locking tools and active
bindings).
spec.ar() now also work for the "ols" method.
(Reported by Hans-Ruedi Kuensch.)
The initialization of objects from S4 subclasses of
"environment" now allocates a new environment object.
R CMD check has more protection against (probably
erroneous) example or test output which is invalid in the current
locale.
qr.X() with column names and pivoting now also pivots
the column names. (PR#14438)
unit.pmax() and unit.pmin() in package
grid gave incorrect results when all inputs were of length 1.
(PR#14443)
The parser for ‘NAMESPACE’ files ignored misspelled directives, rather than signalling an error. For 2.12.x a warning will be issued, but this will be correctly reported as an error in later releases. (Reported by Charles Berry.)
Fix for subsetting of "raster" objects when only one
of i or j is specified.
grid.raster() in package grid did not accept
"nativeRaster" objects (like rasterImage() does).
Rendering raster images in PDF output was resetting the clipping region.
Rendering of raster images on cairo X11 device was wrong, particularly when a small image was being scaled up using interpolation.
With cairo < 1.6, will be better than before, though still a little clunky. With cairo >= 1.6, should be sweet as.
Several bugs fixed in read.DIF(): single column
inputs caused errors, cells marked as "character" could
be converted to other types, and (in Windows) copying from the
clipboard failed.
CHANGES IN R VERSION 2.12.0Reading a package's ‘CITATION’ file now defaults to ASCII rather than Latin-1: a package with a non-ASCII ‘CITATION’ file should declare an encoding in its ‘DESCRIPTION’ file and use that encoding for the ‘CITATION’ file.
difftime() now defaults to the "tzone"
attribute of "POSIXlt" objects rather than to the current
timezone as set by the default for the tz argument. (Wish
of PR#14182.)
pretty() is now generic, with new methods for
"Date" and "POSIXt" classes (based on code
contributed by Felix Andrews).
unique() and match() are now faster on
character vectors where all elements are in the global CHARSXP
cache and have unmarked encoding (ASCII). Thanks to Matthew
Dowle for suggesting improvements to the way the hash code is
generated in ‘unique.c’.
The enquote() utility, in use internally, is exported now.
.C() and .Fortran() now map non-zero return
values (other than NA_LOGICAL) for logical vectors to
TRUE: it has been an implicit assumption that they are
treated as true.
The print() methods for "glm" and "lm"
objects now insert linebreaks in long calls in the same way that
the print() methods for "summary.[g]lm" objects
have long done. This does change the layout of the examples for
a number of packages, e.g. MASS. (PR#14250)
constrOptim() can now be used with method
"SANN". (PR#14245)
It gains an argument hessian to be passed to
optim(), which allows all the ... arguments to be
intended for f() and grad(). (PR#14071)
curve() now allows expr to be an object of
mode "expression" as well as "call" and
"function".
The "POSIX[cl]t" methods for Axis() have been
replaced by a single method for "POSIXt".
There are no longer separate plot() methods for
"POSIX[cl]t" and "Date": the default method has
been able to handle those classes for a long time. This
inter alia allows a single date-time object to be
supplied, the wish of PR#14016.
The methods had a different default ("") for xlab.
Classes "POSIXct", "POSIXlt" and
"difftime" have generators .POSIXct(),
.POSIXlt() and .difftime(). Package authors are
advised to make use of them (they are available from R 2.11.0) to
proof against planned future changes to the classes.
The ordering of the classes has been changed, so "POSIXt"
is now the second class. See the document ‘Updating
packages for changes in R 2.12.x’ on
http://developer.r-project.org for the consequences for a
handful of CRAN packages.
The "POSIXct" method of as.Date() allows a
timezone to be specified (but still defaults to UTC).
New list2env() utility function as an inverse of
as.list(<environment>) and for fast multi-assign()
to existing environment. as.environment() is now generic
and uses list2env() as list method.
There are several small changes to output which ‘zap’
small numbers, e.g. in printing quantiles of residuals in
summaries from "lm" and "glm" fits, and in test
statistics in print.anova().
Special names such as "dim", "names", etc, are
now allowed as slot names of S4 classes, with "class" the
only remaining exception.
File ‘.Renviron’ can have architecture-specific versions such as ‘.Renviron.i386’ on systems with sub-architectures.
installed.packages() has a new argument
subarch to filter on sub-architecture.
The summary() method for packageStatus() now
has a separate print() method.
The default summary() method returns an object
inheriting from class "summaryDefault" which has a
separate print() method that calls zapsmall() for
numeric/complex values.
The startup message now includes the platform and if used, sub-architecture: this is useful where different (sub-)architectures run on the same OS.
The getGraphicsEvent() mechanism now allows multiple windows
to return graphics events, through the new functions
setGraphicsEventHandlers(), setGraphicsEventEnv(), and
getGraphicsEventEnv(). (Currently implemented in the
windows() and X11() devices.)
tools::texi2dvi() gains an index argument,
mainly for use by R CMD Rd2pdf.
It avoids the use of texindy by texinfo's
texi2dvi >= 1.157, since that does not emulate
'makeindex' well enough to avoid problems with special characters
(such as (, {, !) in indices.
The ability of readLines() and scan() to
re-encode inputs to marked UTF-8 strings on Windows since R 2.7.0
is extended to non-UTF-8 locales on other OSes.
scan() gains a fileEncoding argument to
match read.table().
points() and lines() gain "table"
methods to match plot(). (Wish of PR#10472.)
Sys.chmod() allows argument mode to be a
vector, recycled along paths.
There are |, & and xor() methods for
classes "octmode" and "hexmode", which work
bitwise.
Environment variables R_DVIPSCMD, R_LATEXCMD,
R_MAKEINDEXCMD, R_PDFLATEXCMD are no longer used
nor set in an R session. (With the move to
tools::texi2dvi(), the conventional environment variables
LATEX, MAKEINDEX and PDFLATEX will be used.
options("dvipscmd") defaults to the value of DVIPS,
then to "dvips".)
New function isatty() to see if terminal connections are
redirected.
summaryRprof() returns the sampling interval in
component sample.interval and only returns in
by.self data for functions with non-zero self times.
print(x) and str(x) now indicate if an empty
list x is named.
install.packages() and remove.packages() with
lib unspecified and multiple libraries in
.libPaths() inform the user of the library location used
with a message rather than a warning.
There is limited support for multiple compressed streams on a
file: all of [bgx]zfile() allow streams to be appended to an
existing file, but bzfile() reads only the first stream.
Function person() in package utils now uses
a given/family scheme in preference to first/middle/last, is
vectorized to handle an arbitrary number of persons, and gains a
role argument to specify person roles using a controlled
vocabulary (the MARC relator terms).
Package utils adds a new "bibentry" class
for representing and manipulating bibliographic information in
enhanced BibTeX style, unifying and enhancing the previously
existing mechanisms.
A bibstyle() function has been added to the
tools package with default JSS style for rendering
"bibentry" objects, and a mechanism for registering other
rendering styles.
Several aspects of the display of text help are now
customizable using the new Rd2txt_options() function.
options("help_text_width") is no longer used.
Added \href tag to the Rd format, to allow hyperlinks to URLs without displaying the full URL.
Added \newcommand and \renewcommand tags to the Rd format, to allow user-defined macros.
New toRd() generic in the tools package to
convert objects to fragments of Rd code, and added
"fragment" argument to Rd2txt(), Rd2HTML(),
and Rd2latex() to support it.
Directory ‘R_HOME/share/texmf’ now follows the TDS
conventions, so can be set as a texmf tree (‘root
directory’ in MiKTeX parlance).
S3 generic functions now use correct S4 inheritance when
dispatching on an S4 object. See ?Methods, section on
“Methods for S3 Generic Functions” for recommendations
and details.
format.pval() gains a ... argument to pass
arguments such as nsmall to format(). (Wish of
PR#9574)
legend() supports title.adj. (Wish of
PR#13415)
Added support for subsetting "raster" objects, plus
assigning to a subset, conversion to a matrix (of colour
strings), and comparisons (== and !=).
Added a new parseLatex() function (and related
functions deparseLatex() and latexToUtf8()) to
support conversion of bibliographic entries for display in R.
Text rendering of \itemize in help uses a Unicode bullet in UTF-8 and most single-byte Windows locales.
Added support for polygons with holes to the graphics
engine. This is implemented for the pdf(),
postscript(), x11(type="cairo"), windows(),
and quartz() devices (and associated raster formats),
but not for x11(type="Xlib") or xfig() or
pictex(). The user-level interface is the
polypath() function in graphics and
grid.path() in grid.
File ‘NEWS’ is now generated at installation with a slightly different format: it will be in UTF-8 on platforms using UTF-8, and otherwise in ASCII. There is also a PDF version, ‘NEWS.pdf’, installed at the top-level of the R distribution.
kmeans(x, 1) now works. Further, kmeans now
returns between and total sum of squares.
arrayInd() and which() gain an argument
useNames. For arrayInd, the default is now false,
for speed reasons.
As is done for closures, the default print method for
the formula class now displays the associated environment if it is
not the global environment.
A new facility has been added for inserting code into a
package without re-installing it, to facilitate testing
changes which can be selectively added and backed out. See
?insertSource.
New function readRenviron to (re-)read files in the
format of ‘~/.Renviron’ and ‘Renviron.site’.
require() will now return FALSE (and not fail)
if loading the package or one of its dependencies fails.
aperm() now allows argument perm to be a
character vector when the array has named dimnames (as the results
of table() calls do). Similarly, array() allows
MARGIN to be a character vector. (Based on suggestions of
Michael Lachmann.)
Package utils now exports and documents functions
aspell_package_Rd_files() and
aspell_package_vignettes() for spell checking package Rd
files and vignettes using Aspell, Ispell or Hunspell.
Package news can now be given in Rd format, and
news() prefers these ‘inst/NEWS.Rd’ files to old-style
plain text ‘NEWS’ or ‘inst/NEWS’ files.
New simple function packageVersion().
The PCRE library has been updated to version 8.10.
The standard Unix-alike terminal interface declares its name to readline as 'R', so that can be used for conditional sections in ‘~/.inputrc’ files.
‘Writing R Extensions’ now stresses that the standard sections in ‘.Rd’ files (other than \alias, \keyword and \note) are intended to be unique, and the conversion tools now drop duplicates with a warning.
The ‘.Rd’ conversion tools also warn about an unrecognized type in a \docType section.
ecdf() objects now have a quantile() method.
format() methods for date-time objects now attempt to make
use of a "tzone" attribute with "%Z" and
"%z" formats, but it is not always possible. (Wish of
PR#14358.)
tools::texi2dvi(file, clean = TRUE) now works in more
cases (e.g. where emulation is used and when ‘file’ is not in
the current directory).
New function droplevels() to remove unused factor levels.
system(command, intern = TRUE) now gives an error on
a Unix-alike (as well as on Windows) if command cannot be
run. It reports a non-success exit status from running
command as a warning.
On a Unix-alike an attempt is made to return the actual exit
status of the command in system(intern = FALSE): previously
this had been system-dependent but on POSIX-compliant systems the
value return was 256 times the status.
system() has a new argument ignore.stdout
which can be used to (portably) ignore standard output.
system(intern = TRUE) and pipe() connections
are guaranteed to be available on all builds of R.
Sys.which() has been altered to return "" if
the command is not found (even on Solaris).
A facility for defining reference-based S4 classes (in the
OOP style of Java, C++, etc.) has been added experimentally to
package methods; see ?ReferenceClasses.
The predict method for "loess" fits gains an
na.action argument which defaults to na.pass rather
than the previous default of na.omit.
Predictions from "loess" fits are now named from the row
names of newdata.
Parsing errors detected during Sweave() processing
will now be reported referencing their original location in the
source file.
New adjustcolor() utility, e.g., for simple
translucent color schemes.
qr() now has a trivial lm method with a
simple (fast) validity check.
An experimental new programming model has been added to
package methods for reference (OOP-style) classes and
methods. See ?ReferenceClasses.
bzip2 has been updated to version 1.0.6 (bug-fix release). --with-system-bzlib now requires at least version 1.0.6.
R now provides ‘jss.cls’ and ‘jss.bst’ (the class
and bib style file for the Journal of Statistical Software) as
well as ‘RJournal.bib’ and ‘Rnews.bib’, and
R CMD ensures that the ‘.bst’ and ‘.bib’ files
are found by BibTeX.
Functions using the TAR environment variable no longer
quote the value when making system calls. This allows
values such as tar --force-local, but does require
additional quotes in, e.g., TAR = "'/path with spaces/mytar'".
Supplying the parser with a character string containing both octal/hex and Unicode escapes is now an error.
File extension ‘.C’ for C++ code files in packages is now defunct.
R CMD check no longer supports configuration
files containing Perl configuration variables: use the environment
variables documented in ‘R Internals’ instead.
The save argument of require() now defaults to
FALSE and save = TRUE is now deprecated. (This
facility is very rarely actually used, and was superseded by the
Depends field of the ‘DESCRIPTION’ file long ago.)
R CMD check --no-latex is deprecated in favour of
--no-manual.
R CMD Sd2Rd is formally deprecated and will be
removed in R 2.13.0.
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).
When sub-architectures are in use, the installed
architectures are recorded in the Archs field of the
‘DESCRIPTION’ file. There is a new default filter,
"subarch", in available.packages() to make use of
this.
Code is compiled in a copy of the ‘src’ directory when a package is installed for more than one sub-architecture: this avoid problems with cleaning the sources between building sub-architectures.
R CMD INSTALL --libs-only no longer overrides the
setting of locking, so a previous version of the package will be
restored unless --no-lock is specified.
R CMD Rprof|build|check are now based on R rather
than Perl scripts. The only remaining Perl scripts are the
deprecated R CMD Sd2Rd and install-info.pl (used
only if install-info is not found) as well as some
maintainer-mode-only scripts.
NB: because these have been completely rewritten, users should not expect undocumented details of previous implementations to have been duplicated.
R CMD no longer manipulates the environment variables
PERL5LIB and PERLLIB.
R CMD check has a new argument --extra-arch
to confine tests to those needed to check an additional
sub-architecture.
Its check for “Subdirectory 'inst' contains no files” is more thorough: it looks for files, and warns if there are only empty directories.
Environment variables such as R_LIBS and those used for customization can be set for the duration of checking via a file ‘~/.R/check.Renviron’ (in the format used by ‘.Renviron’, and with sub-architecture specific versions such as ‘~/.R/check.Renviron.i386’ taking precedence).
There are new options --multiarch to check the package
under all of the installed sub-architectures and
--no-multiarch to confine checking to the
sub-architecture under which check is invoked. If
neither option is supplied, a test is done of installed
sub-architectures and all those which can be run on the current
OS are used.
Unless multiple sub-architectures are selected, the install done
by check for testing purposes is only of the current
sub-architecture (via R CMD INSTALL --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.)
R CMD build no longer creates an ‘INDEX’ file
(R CMD INSTALL does so), and --force removes
(rather than overwrites) an existing ‘INDEX’ file.
It supports a file ‘~/.R/build.Renviron’ analogously to
check.
It now runs build-time \Sexpr expressions in help files.
R CMD Rd2dvi makes use of tools::texi2dvi()
to process the package manual. It is now implemented entirely in
R (rather than partially as a shell script).
R CMD Rprof now uses utils::summaryRprof()
rather than Perl. It has new arguments to select one of the
tables and to limit the number of entries printed.
R CMD Sweave now runs R with --vanilla so
the environment setting of R_LIBS will always be used.
lang5() and lang6() (in addition to
pre-existing lang[1-4]()) convenience functions for easier
construction of eval() calls. If you have your own
definition, do wrap it inside #ifndef lang5 .... #endif
to keep it working with old and new R.
Header ‘R.h’ now includes only the C headers it itself needs,
hence no longer includes errno.h. (This helps avoid problems
when it is included from C++ source files.)
Headers ‘Rinternals.h’ and ‘R_ext/Print.h’ include the C++ versions of ‘stdio.h’ and ‘stdarg.h’ respectively if included from a C++ source file.
A C99 compiler is now required, and more C99 language features will be used in the R sources.
Tcl/Tk >= 8.4 is now required (increased from 8.3).
System functions access, chdir and
getcwd are now essential to configure R. (In practice
they have been required for some time.)
make check compares the output of the examples
from several of the base packages to reference output rather than
the previous output (if any). Expect some differences due to
differences in floating-point computations between platforms.
File ‘NEWS’ is no longer in the sources, but generated as part of the installation. The primary source for changes is now ‘doc/NEWS.Rd’.
The popen system call is now required to build R.
This ensures the availability of system(intern = TRUE),
pipe() connections and printing from postscript().
The pkg-config file ‘libR.pc’ now also works
when R is installed using a sub-architecture.
R has always required a BLAS that conforms to IE60559 arithmetic, but after discovery of more real-world problems caused by a BLAS that did not, this is tested more thoroughly in this version.
Calls to selectMethod() by default no longer cache
inherited methods. This could previously corrupt methods used by
as().
The densities of non-central chi-squared are now more accurate
in some cases in the extreme tails, e.g. dchisq(2000, 2,
1000), as a series expansion was truncated too early.
(PR#14105)
pt() is more accurate in the left tail for ncp
large, e.g. pt(-1000, 3, 200). (PR#14069)
The default C function (R_binary) for binary ops now
sets the S4 bit in the result if either argument is an S4 object.
(PR#13209)
source(echo=TRUE) failed to echo comments that
followed the last statement in a file.
S4 classes that contained one of "matrix",
"array" or "ts" and also another class now accept
superclass objects in new(). Also fixes failure to call
validObject() for these classes.
Conditional inheritance defined by argument test in
methods::setIs() will no longer be used in S4 method
selection (caching these methods could give incorrect results).
See ?setIs.
The signature of an implicit generic is now used by
setGeneric() when that does not use a definition nor
explicitly set a signature.
A bug in callNextMethod() for some examples with
"..." in the arguments has been fixed. See file
‘src/library/methods/tests/nextWithDots.R’ in the sources.
match(x, table) (and hence %in%) now treat
"POSIXlt" consistently with, e.g., "POSIXct".
Built-in code dealing with environments (get(),
assign(), parent.env(), is.environment() and
others) now behave consistently to recognize S4 subclasses;
is.name() also recognizes subclasses.
The abs.tol control parameter to nlminb()
now defaults to 0.0 to avoid false declarations of
convergence in objective functions that may go negative.
The standard Unix-alike termination dialog to ask whether to
save the workspace takes a EOF response as n to avoid
problems with a damaged terminal connection. (PR#14332)
Added warn.unused argument to hist.default()
to allow suppression of spurious warnings about graphical
parameters used with plot=FALSE. (PR#14341)
predict.lm(), summary.lm(), and indeed
lm() itself had issues with residual DF in zero-weighted
cases (the latter two only in connection with empty
models). (Thanks to Bill Dunlap for spotting the
predict() case.)
aperm() treated resize = NA as resize =
TRUE.
constrOptim() now has an improved convergence
criterion, notably for cases where the minimum was (very close to)
zero; further, other tweaks inspired from code proposals by Ravi
Varadhan.
Rendering of S3 and S4 methods in man pages has been corrected and made consistent across output formats.
Simple markup is now allowed in \title sections in ‘.Rd’ files.
The behaviour of as.logical() on factors (to use the
levels) was lost in R 2.6.0 and has been restored.
prompt() did not backquote some default arguments in
the \usage section. (Reported by Claudia Beleites.)
writeBin() disallows attempts to write 2GB or
more in a single call. (PR#14362)
new() and getClass() will now work if Class
is a subclass of "classRepresentation" and should also be
faster in typical calls.
The summary() method for data frames makes a better
job of names containing characters invalid in the current locale.
[[ sub-assignment for factors could create an invalid
factor (reported by Bill Dunlap).
Negate(f) would not evaluate argument f
until first use of returned function (reported by Olaf Mersmann).
quietly=FALSE is now also an optional argument of
library(), and consequently, quietly is now
propagated also for loading dependent packages, e.g., in
require(*, quietly=TRUE).
If the loop variable in a for loop was deleted, it
would be recreated as a global variable. (Reported by Radford
Neal; the fix includes his optimizations as well.)
Task callbacks could report the wrong expression when the task involved parsing new code. (PR#14368)
getNamespaceVersion() failed; this was an
accidental change in 2.11.0. (PR#14374)
identical() returned FALSE for external
pointer objects even when the pointer addresses were the same.
L$a@x[] <- val did not duplicate in a case it should have.
tempfile() now always gives a random file name (even
if the directory is specified) when called directly after
startup and before the R RNG had been used. (PR#14381)
quantile(type=6) behaved inconsistently. (PR#14383)
backSpline(.) behaved incorrectly when the knot
sequence was decreasing. (PR#14386)
The reference BLAS included in R was assuming that
0*x and x*0 were always zero (whereas they could be
NA or NaN in IEC 60559 arithmetic). This was seen
in results from tcrossprod, and for example that
log(0) %*% 0 gave 0.
The calculation of whether text was completely outside the device region (in which case, you draw nothing) was wrong for screen devices (which have [0, 0] at top-left). The symptom was (long) text disappearing when resizing a screen window (to make it smaller). (PR#14391)
model.frame(drop.unused.levels = TRUE) did not
take into account NA values of factors when deciding to
drop levels. (PR#14393)
library.dynam.unload required an absolute path for
libpath. (PR#14385)
Both library() and loadNamespace() now record
absolute paths for use by searchpaths() and
getNamespaceInfo(ns, "path").
The self-starting model NLSstClosestX failed if some
deviation was exactly zero. (PR#14384)
X11(type = "cairo") (and other devices such as
png using cairographics) and which use Pango font selection
now work around a bug in Pango when very small fonts (those with
sizes between 0 and 1 in Pango's internal units) are requested.
(PR#14369)
Added workaround for the font problem with X11(type =
"cairo") and similar on Mac OS X whereby italic and bold styles
were interchanged. (PR#13463 amongst many other reports.)
source(chdir = TRUE) failed to reset the working
directory if it could not be determined – that is now an error.
Fix for crash of example(rasterImage) on
x11(type="Xlib").
Force Quartz to bring the on-screen display up-to-date
immediately before the snapshot is taken by grid.cap()
in the Cocoa implementation. (PR#14260)
model.frame had an unstated 500 byte limit on
variable names. (Example reported by Terry Therneau.)
The 256-byte limit on names is now documented.
Subassignment by [, [[ or $ on an
expression object with value NULL coerced the object to a
list.
CHANGES IN R VERSION 2.11.1 patchedinstall.packages() has a new optional argument
INSTALL_opts which can be used to pass options to
R CMD INSTALL for source-package installs.
R CMD check now runs the package-specific tests
with LANGUAGE=en to facilitate comparison to
‘.Rout.save’ files.
sessionInfo() gives more detailed platform
information, including 32/64-bit and the sub-architecture if one
is used.
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.
R CMD Rd2dvi failed if run from a path containing
space(s). This also affected R CMD check, which calls
Rd2dvi.
stripchart() could fail with an empty factor
level. (PR#14317)
Text help rendering of \tabular{} has been improved: under some circumstances leading blank columns were not rendered.
strsplit(x, fixed=TRUE) marked UTF-8 strings with the
local encoding when no splits were found.
weighted.mean(NA, na.rm=TRUE) and similar now returns
NaN again, as it did prior to R 2.10.0.
R CMD had a typo in its detection of whether the
environment variable TEXINPUTS was set (reported by Martin
Morgan).
The command-line parser could mistake --file=size... for one of the options for setting limits for Ncells or Vcells.
The internal strptime() could corrupt its copy of the
timezone which would then lead to spurious warnings. (PR#14338)
dir.create(recursive = TRUE) could fail if one of the
components existed but was a directory on a read-only file system.
(Seen on Solaris, where the error code returned is not even listed
as possible on the man page.)
The postscript() and pdf() devices will now
allow lwd values less than 1 (they used to force such
values to be 1).
Fixed font face for CID fonts in pdf() graphics output.
(PR#14326)
GERaster() now checks for width or height of zero and
does nothing in those cases; previously the behaviour was
undefined, probably device-specific, and possibly dangerous.
wilcox.test(x, y, conf.int = TRUE) failed with an unhelpful
message if x and y were constant vectors, and
similarly in the one-sample case. (PR#14329)
Improperly calling Recall() from outside a function
could cause a segfault. (Reported by Robert McGehee.)
\Sexpr[result=rd] in an Rd file added a spurious newline, which was displayed as extra whitespace when rendered.
require(save = TRUE) recorded the names of packages
it failed to load.
packageStatus() could return a data frame with
duplicate row names which could then not be printed.
txtProgressBar(style = 2) did not work correctly.
txtProgressBar(style = 3) did not display until a
non-minimum value was set.
contour() did not display dashed line types
properly when contour lines were labelled. (Reported by
David B. Thompson.)
tools::undoc() again detects undocumented data
objects. Of course, this also affects R CMD check.
ksmooth(x,NULL) no longer segfaults.
approxfun(), approx(), splinefun()
and spline() could be confused by x values that
were different but so close as to print identically.
(PR#14377)
CHANGES IN R VERSION 2.11.1R CMD INSTALL checks if dependent packages are
available early on in the installation of source packages,
thereby giving clearer error messages.
R CMD INSTALL --build now names the file in the
format used for Mac OS X binary files on that platform.
BIC() in package stats4 now also works with
multiple fitted models, analogously to AIC().
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).
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).
The C function mkCharLenCE now no longer reads past
len bytes (unlikely to be a problem except in user
code). (PR#14246)
On systems without any default LD_LIBRARY_PATH (not even ‘/usr/local/lib’), [DY]LIB_LIBRARY_PATH is now set without a trailing colon. (PR#13637)
More efficient implementation of utf8ToInt() on long
multi-byte strings with many multi-byte characters. (PR#14262)
aggregate.ts() gave platform-dependent results due to
rounding error for ndeltat != 1.
package.skeleton() sometimes failed to fix filenames
for ‘.R’ or ‘.Rd’ files to start with an alphanumeric.
(PR#14253)
It also failed when only an S4 class without any methods was defined. (PR#14280)
splinefun(method = "monoH.FC") was not
quite monotone in rare cases. (PR#14215)
Rhttpd no longer crashes due to SIGPIPE when
the client closes the connection prematurely. (PR#14266)
format.POSIXlt() could cause a stack overflow and
crash when used on very long vectors. (PR#14267)
Rd2latex() incorrectly escaped special characters in
\usage sections.
mcnemar.test() could alter the levels (dropping
unused levels) if passed x and y as factors
(reported by Greg Snow).
Rd2pdf sometimes needed a further
pdflatex pass to get hyperlinked pages correct.
interaction() produced malformed results when levels were
duplicated, causing segfaults in split().
cut(d, breaks = <n>) now also works for "Date"
or "POSIXt" argument d.
(PR#14288)
memDecompress() could decompress incompletely rare
xz-compressed input due to incorrect documentation of
xz utils. (Report and patch from Olaf Mersmann.)
The S4 initialize() methods for "matrix",
"array", and "ts" have been fixed to call
validObject(). (PR#14284)
R CMD INSTALL now behaves the same way with or
without --no-multiarch on platforms with only one
installed architecture. (It used to clean the ‘src’
directory without --no-multiarch.)
[<-.data.frame was not quite careful enough in
assigning (and potentially deleting) columns
right-to-left. (PR#14263)
rbeta(n, a, b) no longer occasionally returns
NaN for a >> 1 > b. (PR#14291)
pnorm(x, log.p = TRUE) could return NaN not
-Inf for x near (minus for lower.tail=TRUE)
the largest representable number.
Compressed data files ‘*.(txt|tab|csv).(gz|bz2|xz)’
were not recognized for the list of data topics and hence for
packages using LazyData. (PR#14273)
textConnection() did an unnecessary translation on
strings in a foreign encoding (e.g. UTF-8 strings on Windows) and
so was slower than it could have been on very long input strings.
(PR#14286)
tools::Rd2txt() did not render poorly written Rd
files consistently with other renderers.
It computed widths of strings that would be print()ed with
escapes incorrectly, for example in the computation of column
width for \tabular.
na.action() did not extract the na.action
component as documented.
do.call()ing NextMethod in erroneous ways no
longer segfaults. (PR#13487)
CHANGES IN R VERSION 2.11.0Packages must have been installed under R >= 2.10.0, as the current help system is the only one now supported.
A port to 64-bit Windows is now available as well as binary package repositories: see the ‘R Administration and Installation Manual’.
Argument matching for primitive functions is now done in the same way as for interpreted functions except for the deliberate exceptions
call switch .C .Fortran .Call .External
all of which use positional matching for their first argument,
and also some internal-use-only primitives.
The default device for command-line R at the console on Mac OS X
is now quartz() and not X11().
The open modes for connections are now interpreted
more consistently. open = "r" is now equivalent to
open = "rt" for all connections. The default open =
"" now means "rt" for all connections except the
compressed-file connections gzfile(), bzfile() and
xzfile() for which it means "rb".
R CMD INSTALL now uses the internal untar()
function in package utils: this ensures that all platforms
can install bzip2- and xz-compressed
tarballs. In case this causes problems (as it has on some
Windows file systems when run from Cygwin tools) it can be
overridden by the environment variable R_INSTALL_TAR:
setting this to a modern external tar program will speed up
unpacking of large (tens of Mb or more) tarballs.
help(try.all.packages = TRUE) is much faster
(although the time taken by the OS to find all the packages the
first time it is used can dominate the time).
R CMD check has a new option --timings
to record per-example timings in file
‘<pkg>.Rcheck/<pkg>-Ex.timings’.
The TRE library has been updated to version 0.8.0 (minor bugfixes).
grep[l], [g]sub and [g]regexpr now work
in bytes in an 8-bit locales if there is no marked UTF-8 input
string: this will be somewhat faster, and for [g]sub()
give the result in the native encoding rather than in UTF-8
(which returns to the behaviour prior to R 2.10.0).
A new argument skipCalls has been added to
browser() so that it can report the original context when
called by other debugging functions.
More validity checking of UTF-8 and MBCS strings is done by
agrep() and the regular-expression matching functions.
The undocumented restriction on gregexpr() to
length(text) > 0 has been removed.
Package tcltk now sends strings to Tcl in UTF-8: this means that strings with a marked UTF-8 encoding are supported in non-UTF-8 locales.
The graphics engine now supports rendering of raster (bitmap)
images, though not all graphics devices can provide (full)
support. Packages providing graphics devices (e.g., Cairo,
RSvgDevice, cairoDevice) will need to be reinstalled.
There is also support in the graphics engine for capturing raster images from graphics devices (again not supported on all graphics devices).
R CMD check now also checks if the package and
namespace can be unloaded: this provides a check of the
.Last.lib() and .onUnload() hook functions (unless
--install=fake).
prop.table(x) now accepts a one-dimensional table for
x.
A new function vapply() has been added, based on a
suggestion from Bill Dunlap. It requires that a template for the
function value be specified, and uses it to determine the output
type and to check for consistency in the function values.
The main HTML help page now links to a reformatted copy of this ‘NEWS’ file. (Suggested by Henrik Bengtsson.) Package index files link to the package ‘DESCRIPTION’ and ‘NEWS’ files and a list of demos when using dynamic help.
The [ method for class "AsIs" allows the next
method to change the underlying class. (Wish of Jens
Oehlschlägel.)
write.csv[2] no longer allow argument append
to be changed: as ever, direct calls to write.table() give
more flexibility as well as more room for error.
The index page for HTML help for a package now collapses multiple signatures for S4 methods into a single entry.
The use of .required by require() and
detach() has been replaced by .Depends which is set
from the Depends field of a package (even in packages with
namespaces). By default detach() prevents such
dependencies from being detached: this can be overridden by the
argument force.
bquote() has been extended to work on function
definitions. (Wish of
PR#14031).
detach() when applied to an object other than a
package returns the environment that has been detached, to
parallel attach().
readline() in non-interactive use returns ""
and does not attempt to read from the ‘terminal’.
New function file_ext() in package tools.
xtfrm() is now primitive and internally generic, as
this allows S4 methods to be set on it without name-space scoping
issues.
There are now "AsIs" and "difftime" methods, and
the default method uses unclass(x) if is.numeric(x)
is true (which will be faster but relies on is.numeric()
having been set correctly for the class).
is.numeric(x) is now false for a "difftime"
object (multiplication and division make no sense for such
objects).
The default method of weighted.mean(x, w) coerces
w to be numeric (aka double); previously only integer
weights were coerced. Zero weights are handled specially so an
infinite value with zero weight does not force an NaN
result.
There is now a "difftime" method.
bug.report() now has arguments package and
lib.loc to generate bug reports about packages. When
this is used, it looks for a BugReports field in the
package ‘DESCRIPTION’ file, which will be assumed to be a
URL at which to submit the report, and otherwise generates an
email to the package maintainer. (Suggested by Barry
Rowlingson.)
quantile() now has a method for the date-time class
"POSIXt", and types 1 and 3 (which never interpolate) work
for Dates and ordered factors.
length(<POSIXlt>) now returns the length of the
corresponding abstract timedate-vector rather than always 9 (the
length of the underlying list structure). (Wish of PR#14073
and PR#10507.)
The readline completion backend no longer sorts
possible completions alphabetically (e.g., function argument
names) if R was built with readline >= 6.
select.list() gains a graphics argument to
allow Windows/Mac users to choose the text interface. This
changes the behaviour of new.packages(ask=TRUE) to be like
update.packages(ask=TRUE) on those platforms in using a
text menu: use ask="graphics" for a graphical menu.
New function chooseBioCmirror() to set the
"BioC_mirror" option.
The R grammar now prevents using the argument name
in signatures of S4 methods for $ and $<-, since
they will always be called with a character string value for
name. The implicit S4 generic functions have been
changed to reflect this: packages which included name in
the signature of their methods need to be updated and
re-installed.
The handling of the method argument of glm()
has been refined following suggestions by Ioannis Kosmidis and
Heather Turner.
str() gains a new argument list.len with
default 99, limiting the number of list() items (per
level), thanks to suggestions from David Winsenius.
Having formal arguments of an S4 method in a different order from the generic is now an error (the warning having been ignored by some package maintainers for a long time).
New functions enc2native() and enc2utf8()
convert character vectors with possibly marked encodings to the
current locale and UTF-8 respectively.
Unrecognized escapes and embedded nuls in character strings are
now an error, not just a warning. Thus option "warnEscapes"
is no longer needed. rawToChar() now removes trailing nuls
silently, but other embedded nuls become errors.
Informational messages about masked objects displayed when a
package is attached are now more compact, using strwrap()
instead of one object per line.
print.rle() gains argument prefix.
download.file() gains a "curl" method, mainly
for use on platforms which have curl but not
wget, but also for some hard-to-access URLs.
In Rd, \eqn and \deqn will render in
HTML (and convert to text) upper- and lower-case Greek letters
(entered as \alpha ...), \ldots, \dots,
\ge and \le.
utf8ToInt() and intToUtf8() now map NA inputs
to NA outputs.
file() has a new argument raw which may help
if it is used with something other than a regular file, e.g. a
character device.
New function strtoi(), a wrapper for the C function
strtol.
as.octmode() and as.hexmode() now allow inputs
of length other than one.
The format() and print() methods for
"octmode" now preserve names and dimensions (as those for
"hexmode" did).
The format() methods for classes "octmode" and
"hexmode" gain a width argument.
seq.int() returns an integer result in some further cases
where seq() does, e.g. seq.int(1L, 9L, by = 2L).
Added \subsection{}{} macro to Rd syntax, for subsections within sections.
n-dimensional arrays with dimension names can now be indexed
by an n-column character matrix. The indices are matched against
the dimension names. NA indices are propagated to the
result. Unmatched values and "" are not allowed and
result in an error.
interaction(drop=TRUE) uses less memory (related to
PR#14121).
summary() methods have been added to the
"srcref" and "srcfile" classes, and various
encoding issues have been cleaned up.
If option "checkPackageLicense" is set to TRUE (not
currently the default), users will be asked to agree to
non-known-to-be-FOSS package licences at first use.
Checking setAs(a, b) methods only gives a message
instead of a warning, when one of a or b is
unknown.
New function norm() to compute a matrix norm.
norm() and also backsolve() and sample()
have implicit S4 generics.
Files ‘Renviron.site’ and ‘Rprofile.site’ can have architecture-specific versions on systems with sub-architectures.
R CMD check now (by default) also checks Rd files
for auto-generated content in need of editing, and missing
argument descriptions.
aggregate() gains a formula method thanks to a
contribution by Arni Magnusson. The data frame method now allows
summary functions to return arbitrarily many values.
path.expand() now propagates NA values rather
than converting them to "NA".
file.show() now disallows NA values for file names,
headers, and pager.
The ‘fuzz’ used by seq() and seq.int() has
been reduced from 1e-7 to 1e-10, which should be
ample for the double-precision calculations used in R. It
ensures that the fuzz never comes into play with sequences of
integers (wish of PR#14169).
The default value of RSiteSearch(restrict=) has been
changed to include vignettes but to exclude R-help. The R-help
archives available have been split, with a new option of
"Rhelp10" for those from 2010.
New function rasterImage() in the graphics
package for drawing raster images.
stats:::extractAIC.coxph() now omits aliased terms
when computing the degrees of freedom (suggestion of Terry
Therneau).
cor() and cov() now test for misuse with
non-numeric arguments, such as the non-bug report PR#14207.
pchisq(ncp =, log.p = TRUE) is more accurate for
probabilities near one. E.g. pchisq(80, 4, ncp=1,
log.p=TRUE). (Maybe what was meant in PR#14216.)
maintainer() has been added, to give convenient
access to the name of the maintainer of a package (contributed by
David Scott).
sample() and sample.int() allow zero items to
be sampled from a zero-length input. sample.int() gains a
default value size=n to be more similar to
sample().
switch() returned NULL on error (not
previously documented on the help page): it now does so
invisibly, analogously to if-without-else.
It is now primitive: this means that argument EXPR is
always matched to the first argument and there is no danger of
partial matching to later named arguments.
Primitive functions UseMethod(), attr(),
attr<-(), on.exit(), retracemem() and
substitute() now use standard argument matching (rather
than positional matching). This means that all multi-argument
primitives which are not internal now use standard argument
matching except where positional matching is desirable (as for
switch(), call(), .C() ...).
All the one-argument primitives now check that any name supplied for their first argument is a partial match to the argument name as documented on the help page: this also applies to replacement functions of two arguments.
base::which() uses a new .Internal function
when arr.ind is FALSE resulting in a 10x speedup.
Thanks to Patrick Aboyoun for implementation suggestions.
Help conversion to text now uses the first part of
\enc{}{} markup if it is representable in the current
output encoding. On the other hand, conversion to LaTeX with the
default outputEncoding = "ASCII" uses the second part.
A new class "listOfMethods" has been introduced to
represent the methods in a methods table, to replace the
deprecated class "MethodsList".
any() and all() return early if possible.
This may speed up operations on long vectors.
strptime() now accepts "%z" (for the offset
from UTC in the RFC822 format of +/-hhmm).
The PCRE library has been updated to version 8.02, a bug-fix release which also updates tables to Unicode 5.02.
Functions which may use a graphical select.list()
(including menu() and install.packages()) now check
on a Unix-alike that Tk can be started (and not just
capabilities("tcltk") && capabilities("X11")).
The parser no longer marks strings containing octal or hex escapes as being in UTF-8 when entered in a UTF-8 locale.
On platforms with cairo but not Pango (notably Mac OS X) the
initial default X11() type is set to "Xlib": this avoids
several problems with font selection when done by cairo rather
than Pango (at least on Mac OS X).
New function arrayInd() such that which(x,
arr.ind = TRUE) for an array 'x' is now equivalent to
arrayInd(which(x), dim(x), dimnames(x)).
Bundles of packages are defunct.
stats::clearNames() is defunct: use unname().
Basic regular expressions are defunct, and
strsplit(), grep(), grepl(), sub(),
gsub(), regexpr() and gregexpr() no longer
have an extended argument.
methods::trySilent() is defunct.
index.search() (which was deprecated in 2.10.0) is no
longer exported and has a different argument list.
Use of multiple arguments to return() is now defunct.
The use of UseMethod() with more than two arguments
is now defunct.
In the methods package, the "MethodsList"
metadata objects which had been superseded by hash tables
(environments) since R 2.8.0 are being phased out. Objects of
this class are no longer assigned or used as metadata by the
package.
getMethods() is now deprecated, with its internal use replaced
by findMethods() and other changes. Creating objects from the
"MethodsList" class is also deprecated.
Parsing strings containing both octal/hex and Unicode escapes now gives a warning and will become an error in R 2.12.0.
UTF-8 is now used for the reference manual and package manuals. This requires LaTeX ‘2005/12/01’ or later.
configure looks for a POSIX compliant
tr, Solaris's /usr/ucb/tr having been found
to cause Rdiff to malfunction.
configure is now generated with autoconf
2.65, which works better on recent systems and on Mac OS X.
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.
R CMD INSTALL now tests that the installed package
can be loaded (and backs out the installation if it cannot): this
can be suppressed by --no-test-load. This avoids
installing/updating a package that cannot be used: common causes
of failures to load are missing/incompatible external software
and missing/broken dependent packages.
Package installation on Windows for a package with a ‘src’ directory now checks if a DLL is created unless there is a ‘src/Makefile.win’ file: this helps catch broken installations where the toolchain has not reported problems in building the DLL. (Note: this can be any DLL, not just one named ‘<pkg-name>.dll’.)
Using with(), eval() etc with a list with some
unnamed elements now works.
(PR#14035)
The "quick" dispatch of S4 methods for primitive
functions was not happening, forcing a search each time.
(Dispatch for closures was not affected.) A side effect is that
default values for arguments in a method that do not have
defaults in the generic will now be ignored.
Trying to dispatch S4 methods for primitives during the search
for inherited methods slows that search down and potentially
could cause an infinite recursion. An internal switch was
added to turn off all such methods from
findInheritedMethods().
R framework installation (on Mac OS X) would not work
properly if a rogue Resources directory was present at the
top level. Such a non-symlink will now be renamed to
Resources.old (and anything previously named
Resources.old removed) as part of the framework
installation process.
The checks for conforming S4 method arguments could fail
when the signature of the generic function omitted some of the
formal arguments (in addition to ...). Arguments omitted
from the method definition but conforming (per the documentation)
should now be ignored (treated as "ANY") in dispatching.
The computations for S4 method evaluation when ...
was in the signature could fail, treating ... as an
ordinary symbol. This has been fixed, for the known cases.
Various ar() fitting methods have more protection for
singular fits.
callNextMethod now works again with the drop=
argument in [
parse() and parse_Rd() miscounted columns when
multibyte UTF-8 characters were present.
Formatting of help pages has had minor improvements: extra blank lines have been removed from the text format, and empty package labels removed from HTML.
cor(A, B) where A is n x 1
and B a 1-dimensional array segfaulted or gave an internal
error. (The case cor(B, A) was
PR#7116.)
cut.POSIXt() applied to a start value after the DST
transition on a DST-change day could give the wrong time for
argument breaks in units of days or longer. (PR#14208)
do_par() UNPROTECTed too early (PR#14214)
Subassignment x[[....]] <- y didn't check for a
zero-length right hand side, and inserted a rubbish
value. (PR#14217)
fisher.test() no longer gives a P-value very
slightly > 1, in some borderline cases.
Internal function matchArgs() no longer modifies the
general purpose bits of the SEXPs that make up the formals
list of R functions. This fixes an invalid error message that
would occur when a garbage collection triggered a second call to
matchArgs for the same function via a finalizer.
gsub() in 2.10.x could fail from stack overflow for
extremely long strings due to temporary data being allocated on
the stack. Also, gsub() with fixed=TRUE is in some
circumstances considerably faster.
Several primitives, including attributes(),
attr<-() interactive(), nargs() and
proc.time(), did not check that they were called with the
correct number of arguments.
A potential race condition in list.files() when other
processes are operating on the directory has been fixed; the code
now dynamically allocates memory for file listings in a single
pass instead of making an initial count pass.
mean(x, trim=, na.rm = FALSE) failed to return NA if
x contained missing values. (Reported by Bill Dunlap.)
Extreme tail behavior of, pbeta() {and hence
pf()}, e.g., pbeta(x, 3, 2200, lower.tail=FALSE,
log.p=TRUE) now returns finite values instead of jumping to
-Inf too early. (PR#14230).
parse(text=x) misbehaved for objects x that
were not coerced internally to character, notably symbols.
(Reported to R-devel by Bill Dunlap.)
The internal C function coerceSymbol now handles
coercion to character, and warns if coercion fails (rather than
silently returning NULL). This allows a name to be given
where a character vector is required in functions which coerce
internally.
The interpretation by strptime() of "%c" was
non-standard (not that it is ever advisable to use locale- and
system-specific input formats).
capabilities("X11") now works the same way on Mac OS X as on
other platforms (and as documented: it was always true for R
built with --with-aqua, as the CRAN builds are).
The X11() device with cairo but not Pango (notably Mac OS X)
now checks validity of text strings in UTF-8 locales (since
Pango does but cairo it seems does not).
read.fwf() misread multi-line records when n was specified.
(PR#14241)
all.equal(tolerance = e) passes the numeric
tolerance also to the comparison of the attributes.
pgamma(0, 0), a boundary case, now returns 0, its
limit from the left, rather than the limit from the right.
Issuing POST requests to the internal web server could stall
the request under certain circumstances.
gzcon( <textConnection> ), an error, no longer
damages the connection (in a way to have it
segfault). (PR#14237)
All the results from hist() now use the nominal
breaks not those adjusted by the numeric ‘fuzz’:
in recent versions the nominal breaks were reported but
the 'density' referred to the intervals used in the calculation
– which mattered very slightly for one of the extreme bins.
(Based on a report by Martin Becker.)
If xy[z].coords (used internally by many graphics
functions) are given a list as x, they now check that
the list has suitable names and give a more informative error
message. (PR#13936)
CHANGES IN R VERSION 2.10.1 patched The handling of line textures in the postscript() and
pdf() devices was set up for round end caps (the only type
which existed at the time): it has now been adjusted for butt
endcaps.
lchoose(a, k) is now defined as
log(abs(choose(a,k))), analogously to lfactorial().
Although \eqn{} in Rd files is defined as a
‘verbatim’ macro, many packages expected \dots 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).
Escaping of braces in quoted strings in R-code sections of Rd files is allowed again. This had been changed for the new Rd format in R 2.10.0 but was only documented on the developer site and was handled inconsistently by the converters: text and example conversion removed the escapes but HTML conversion did not.
The PCRE library has been updated to version 8.01, a bug-fix release.
tools::readNEWS() now accepts a digit as the first
character of a news section.
Using read.table(header=TRUE) on a header with an
embedded new line would copy part of the header into the data.
(PR#14103)
qpois(p = 1, lambda = 0) now gives 0 as for all other
p. (PR#14135)
Functions related to string comparison
(e.g. unique(), match()) could cause crashes when
used with strings not in the native encoding, e.g. UTF-8 strings
on Windows. (PR#14114 and PR#14125)
x[ , drop=TRUE] dropped an NA level even if it
was in use.
The dynamic HTML help system reported the wrong MIME type for the style sheet.
tools::codoc() (used by R CMD check) was
missing cases where the function had no arguments but was
documented to have some.
Help links containing special characters (e.g. "?")
were not generated correctly when rendered in
HTML. (PR#14155)
lchoose(a, k) no longer wrongly gives NaN for
negative a.
ks.test() could give a p-value that was off by one
observation due to rounding error. (PR#14145)
readBin()/readChar() when reading millions of
character strings in a single call used excessive amounts of
memory (which also slowed them down).
R CMD SHLIB could fail if used with paths that
were not alphanumeric, e.g. contained +. (PR#14168)
sprintf() was not re-entrant, which potentially
caused problems if an as.character() method called it.
The quartz() device did not restore the clipping
region when filling the background for a new page. This could be
observed in multi-page bitmap output as stale outer regions of
the plot.
p.adjust(method, n) now works correctly for the
rare case n > length(p), also when method differs from
"bonferroni" or "none", thanks to a patch from
Gordon Smyth.
tools::showNonASCII() failed to detect non-ASCII characters
if iconv() (incorrectly) converted them to different ASCII
characters. (Seen on Windows only.)
tcrossprod() wrongly failed in some cases when one of the
arguments was a vector and the other a matrix.
[cr]bind(..., deparse.level=2) was not always giving
names when documented to do so. (Discovered whilst investigating
PR#14189.)
match(incomparables=<non-NULL>) could in rare cases
infinite-loop.
poisson.test() needed to pass argument
conf.level to binom.test(). (PR#14195)
The "nls" method for df.residual() gave
incorrect results for models fitted with na.action =
na.exclude. (PR#14194)
A change to options(scipen=) was only implemented
when printing next occurred, even though it should have affected
intervening calls to axis(), contour() and
filledcontour().
prettyNum(drop0trailing=TRUE) did not handle signs of
imaginary parts of complex numbers correctly (and this was used
by str(): PR#14201).
system.time() had the sys.child component
wrong (copied user.child instead) on systems with
HAVE_GETRUSAGE.
(PR#14210)
Changing both line texture and line cap (end) resulted in the latter to be omitted form the PDF code. In addition, line cap (end) and join are now set explicitly in PDF output to ensure correct defaults.
The suppression of auto-rotation in bitmap() and
dev2bitmap() with the "pdfwrite" device was not
working correctly.
plot(ecdf(), log="x") no longer gives an incorrect
warning.
read.fwf() works again when argument file is
a connection.
Startup files will now be found if their paths exceed 255 bytes. (PR#14228)
contrasts<- (in the stats package) no longer has an
undeclared dependence on methods (introduced in 2.10.0).
CHANGES IN R VERSION 2.10.1The PCRE library has been updated to version 8.00.
R CMD INSTALL has new options --no-R,
--no-libs, --no-data, --no-help,
--no-demo, --no-exec, and --no-inst to
suppress installation of the specified part of the package.
These are intended for special purposes (e.g. building a database
of help pages without fully installing all packages).
The documented line-length limit of 4095 bytes when reading
from the console now also applies also to parse(file="")
(which previously had a limit of around 1024 bytes).
A Bioconductor mirror can be set for use by
setRepositories() via the option "BioC_mirror",
e.g. the European mirror can be selected by
options(BioC_mirror="http://bioconductor.statistik.tu-dortmund.de").
Double-clicking in a tk_select.list() list box now
selects the item and closes the list box (as happens on the
Windows select.list() widget).
configure will be able to find a usable
libtiff in some rare circumstances where it did not
previously (where libtiff needed to be linked explicitly against
-ljpeg).
Making refman.pdf works around a problem with the indexing
with hyperref 6.79d and later.
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.
trigamma(x) and other psigamma(x, n) calls
are now accurate for very large abs(x). (PR#14020)
[g]sub(perl=FALSE, fixed=FALSE) could use excessive
stack space when used with a very long vector containing some
non-ASCII strings.
The default method of weighted.mean(na.rm = TRUE)
did not omit weights for NA observations in 2.10.0.
(PR#14032)
[g]regexpr(pattern, fixed = TRUE) returned match
positions in bytes (not characters) in an MBCS locale if
pattern was a single byte.
[g]sub(fixed = TRUE) with a single-byte pattern could
conceivably have matched part of a multibyte character in a
non-UTF-8 MBCS.
findLineNum() and setBreakpoint() would
sometimes fail if the specified file was not in the current
directory.
Package tcltk's demo(tkdensity) was broken in
2.9.0 when demo() was changed to set par(ask = TRUE).
gsub() with backrefs could fail on extremely long strings
(hundreds of thousands of characters) due to integer overflow
in a length calculation.
abline(untf=TRUE) now uses a better x-grid in
log-scale, e.g., for plot(c(1,300), c(1,300), log="xy");
abline(4,1, untf=TRUE).
detach()/unloadNamespace() arrange to flush
the package's lazyload cache of R objects once the
package/namespace is no longer needed.
There have been small fixes to the rendering of help,
e.g. \command is now rendered verbatim (so e.g. --
is not interpreted, PR#14045).
Also, there are many small changes to help files where the new converters were not rendering them in the same way as before.
available.packages() would fail when run on a
repository with no packages meeting the filtering conditions.
(PR#14042)
rep(x, times, each = 2) gave invalid results when the
times argument was a vector longer than x.
Reported by Bill Dunlap.
An error when unloadNamespace() attempted to run the
.onUnload() function gave an error in the reporting
function and so was not reported properly.
Text help rendering did not handle very long input lines properly.
promptMethods() generated signature documentation
improperly.
pgamma(x, a, lower.tail=FALSE) and
qgamma(...) are now considerably more accurate in some
regions for very small a. qgamma() now correctly
returns 0 instead of NaN in similar extreme cases,
and qgamma() no longer warns in the case of small
a, see (PR#12324).
unname() now also removes names from a zero length vector.
Printing results from ls.str() no longer evaluates
unevaluated calls.
complete.cases() failed on a 0-column data frame
argument. (Underlies PR#14066.)
It could return nonsensical results if no input determined the number of cases (seen in the no-segfault tests).
An error in nls() with a long formula could cause a
segfault. (PR#14059)
qchisq(p, df, ncp, lower.tail = FALSE) with
ncp >= 80 was inaccurate for small p (as the help page
said): it is now less inaccurate. (In part,
PR#13999.)
For ncp less than but close to 80, pchisq() and
qchisq() are more accurate for 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.
intToUtf8() could fail when asked to produce 10Mb or more
strings, something it was never intended to do: unfortunately
Windows crashed R (other OSes reported a lack of resources).
(PR#14068)
chisq.test() could fail when given argument
x or y which deparsed to more than one line.
(Reported by Laurent Gauthier.)
S4 methods are uncached whenever the namespace containing
them is unloaded (by unloadNamespace() as well as by
detach(unload = TRUE)).
The internal record-keeping by
dyn.load/dyn.unload was incomplete, which could
crash R if a DLL that registered .External routines had
earlier been unloaded.
bessel[JY](x, nu) with nu a negative integer (a
singular case) is now correct, analogously to besselI(),
see PR#13556.
tools::file_path_as_absolute() doubled the file
separator when applied to a file such as ‘"/vmunix"’ or (on
Windows) ‘"d:/afile"’ in a directory for which
getwd() would return a path with a trailing separator
(largely cosmetic, as reasonable file systems handle such a path
correctly). (Perhaps what was meant by PR#14078.)
unsplit(drop = TRUE) applied to a data frame failed
to pass drop to the computation of row names. (PR#14084)
The "difftime" method of mean() ignored its
na.rm argument.
tcltk::tk_select.list() is now more likely to remove the
widget immediately after selection is complete.
Adding/subtracting a "difftime" object to/from a
"POSIXt" or "Date" object works again (it was
broken by the addition of Ops.difftime).
Conversion to latex of an Rd file with no aliases failed.
wilcox.test(conf.int=TRUE) has achieved.level
corrected and, for exact=FALSE, now returns a
estimate component which does not depend on the
alternative used.
help.search() failed when the package argument was
specified. (PR#14113)
switch(EXPR = "A") now returns NULL, as does
switch(1) (which used to signal an error).
CHANGES IN R VERSION 2.10.0 Package help is now converted from Rd by the R-based
converters that were first introduced in 2.9.0. This means
Packages that were installed by R-devel after 2009-08-09 should not be used with earlier versions of R, and most aspects of package help (including the runnable examples) will be missing if they are so used.
Text, HTML and latex help and examples for packages installed under the new system are converted on-demand from stored parsed Rd files. (Conversions stored in packages installed under R < 2.10.0 are used if no parsed Rd files are found. It is recommended that such packages be re-installed.)
HTML help is now generated dynamically using an HTTP server running in the R process and listening on the loopback interface.
Those worried about security implications of such
a server can disable it by setting the environment variable
R_DISABLE_HTTPD to a non-empty value. This disables
help.start() and HTML help (so text help is shown
instead).
The Java/Javascript search engine has been replaced by an
HTML interface to help.search(). help.start() no
longer has an argument searchEngine as it is no longer
needed.
The HTML help can now locate cross-references of the form
\link[pkg]{foo} and \link[pkg:foo]{bar}
where foo is an alias in the package, rather than the
documented (basename of a) filename (since the documentation
has been much ignored).
polygon(), pdf() and postscript() now
have an argument fillOddEven (default FALSE),
which controls the mode used for polygon fills of
self-intersecting shapes.
New debugonce() function; further,
getOption("deparse.max.lines") is now observed when
debugging, from a code suggestion by John Brzustowski.
(PR#13647/8)
plot() methods for "stepfun" and hence
"ecdf" no longer plot points by default for n >= 1000.
[g]sub(perl=TRUE) now also supports "\E"
in order to end "\U" and "\L" case changes,
thanks to a patch from Bill Dunlap.
factor(), levels()<-, etc, now ensure that
the resulting factor levels are unique (as was always the implied
intention). Factors with duplicated levels are still
constructible by low-level means, but are now declared illegal.
New print() (S3) method for class "function",
also used for auto-printing. Further, .Primitive
functions now print and auto-print identically. The new method
is based on code suggestions by Romain François.
The print() and toLatex() methods for class
"sessionInfo" now show the locale in a nicer format and
have arguments to suppress locale information.
In addition to previously only round(), there are
other Math group (S3) methods for "difftime",
such as floor(), signif(), abs(), etc.
For completeness, old.packages() and
available.packages() allow arguments type to be
specified (you could always specify arguments available
or contriburl).
available.packages() by default only returns
information on the latest versions of packages whose version
requirements are satisfied by the currently running R.
tools::write_PACKAGES() has a new argument
latestOnly, which defaults to TRUE when only the
latest versions in the repository will be listed in the index.
getOption() has a new argument default that
is returned if the specified option is not set. This simplifies
querying a value and checking whether it is NULL or not.
parse() now warns if the requested encoding is not supported.
The "table" method of as.data.frame() gains a
stringsAsFactors argument to allow the classifying
factors to be returned as character vectors rather than the
default factor type.
If model.frame.default() encounters a character
variable where xlev indicates a factor, it now converts
the variable to a factor (with a warning).
curve() now returns a list containing the points that
w§ere drawn.
spineplot() now accepts axes = FALSE, for
consistency with other functions called by plot.factor().
The Kendall and Spearman methods of cor.test() can
optionally use continuity correction when not computing exact
p-values. (The Kendall case is the wish of PR#13691.)
R now keeps track of line numbers during execution for code
sourced with options(keep.source = TRUE). The source
reference is displayed by debugging functions such as
traceback(), browser(), recover(), and
dump.frames(), and is stored as an attribute on each
element returned by sys.calls().
More functions now have an implicit (S4) generic definition.
quantile.default() now disallows factors (wish of
PR#13631) and its help
documents what numeric-like properties its input need to have to
work correctly.
weighted.mean() is now generic and has "Date",
"POSIXct" and "POSIXlt" methods.
Naming subscripts (e.g. x[i=1, j=2]) in
data.frame methods for [ and [[ now gives a
warning. (Names are ignored in the default method, but could
have odd semantics for other methods, and do for the data.frame
ones.)
as.data.frame() has an "aovproj" method.
(Wish of PR#13505)
as.character(x) for numeric x no longer
produces strings such as "0.30", i.e., with trailing
zeros. This change also renders levels construction in
factor() more consistent.
codocClasses(), which checks consistency of the
documentation of S4 class slots, now does so in considerably more
cases. The documentation of inherited slots (from superclasses)
is now optional. This affects R CMD check <pkg> when
the package defines S4 classes.
codoc() now also checks S4 methods for code/documentation
mismatches.
for(), while(), and repeat() loops now
always return NULL as their (invisible) value. This change was
needed to address a reference counting bug without creating
performance penalties for some common use cases.
The print() method for ls.str() results now
obeys an optional digits argument.
The method argument of glm() now allows
user-contributed methods.
More general reorder.default() replaces functionality of
reorder.factor() and reorder.character().
The function aspell() has been added to provide an
interface to the Aspell spell-checker.
Filters RdTextFilter() and SweaveTeXFilter()
have been added to the tools package to provide support for
aspell() or other spell checkers.
xtabs() with the new argument sparse = TRUE
now returns a sparse Matrix, using package Matrix.
contr.sum() etc gain an argument sparse
which allows sparse matrices to be returned.
contrasts() also gains a sparse argument which it
passes to the actual contrast function if that has a formal
argument sparse.
contrasts(f, .) <- val now also works when val
is a sparse Matrix. It is planned that model.matrix()
will work with such factors f in the future.
readNEWS() will recognize a UTF-8 byte-order mark
(BOM) in the ‘NEWS’ file. However, it is safer to use only
ASCII code there because not all editors recognize BOMs.
New utility function inheritedSlotNames() for S4
class programming.
tabulate() now allows NAs to pass through (and be ignored).
If debug() is called on an S3 generic function then
all methods are debugged as well.
Outlier symbols drawn by boxplot() now obey the
outlwd argument. Reported by Jurgen Kluge.
svd(x) and eigen(x) now behave analogously to
qr(x) in accepting logical matrices x.
File ‘NEWS’ is now in UTF-8, and has a BOM (often
invisible) on the first line, and Emacs local variables
set for UTF-8 at the end. RShowDoc("NEWS") should display
this correctly, given suitable fonts.
terms.formula(simplify = TRUE) now does not deparse
the LHS and so preserves non-standard responses such as `a:
b` (requested by Sundar Dorai-Raj).
New function news() for building and querying R or
package news information.
z^n for integer n and complex z is more
accurate now if |n| <= 65536.
factor(NULL) now returns the same as
factor(character(0)) instead of an error, and
table(NULL) consequently does analogously.
as.data.frame.vector() (and its copies) is slightly faster
by avoiding a copy if there are no names (following a
suggestion of Tim Hesterberg).
writeLines(), writeBin() and
writeChar() have a new argument useBytes. If
false, character strings with marked encodings are translated to
the current locale (as before) but if true they are written
byte-by-byte.
iconv() has a new argument mark which can be
used (by experts) to suppress the declaration of encodings.
‘DESCRIPTION’ file's LinkingTo specs are now
recognized as installation dependencies, and included in package
management computations.
Standardized ‘DESCRIPTION’ file License specs
are now available for package management computations.
"\uxxxx" and "\Uxxxxxxxx" escapes can now be
parsed to a UTF-8 encoded string even in non-UTF-8 locales (this
has been implemented on Windows since R 2.7.0). The semantics
have been changed slightly: a string containing such escapes is
always stored in UTF-8 (and hence is suitable for portably
including Unicode text in packages).
New as.raw() method for "tclObj" objects (wish
of PR#13758).
Rd.sty now makes a better job of setting email addresses,
including using a monospaced font.
textConnection() gains an encoding argument
to determine how input strings with marked encodings will be
handled.
R CMD Rd2pdf is available as a shortcut for
R CMD Rd2dvi --pdf.
R CMD check now checks links where a package is
specified (\link[pkg]{file} or
\link[pkg:file]{topic}), if the package is available.
It notes if the package is not available, as in many cases this
is an error in the link.
identical() gains three logical arguments, which
allow for even more differentiation, notably -0 and
0.
legend() now can specify the border color of
filled boxes, thanks to a patch from Frederic Schutz.
Indexing with a vector index to [[ ]] has now been
extended to all recursive types.
Pairlists may now be assigned as elements of lists. (Lists
could always be created with pairlist elements, but [[<-
didn't support assigning them.)
The parser now supports C-preprocessor-like #line
directives, so error messages and source references may refer to
the original file rather than an intermediate one.
New functions findLineNum() and
setBreakpoint() work with the source references to find
the location of source lines and set breakpoints (using
trace()) at those lines.
Namespace importing is more careful about warning on masked generics, thanks to a patch by Yohan Chalabi.
detach() now has an argument character.only
with the same meaning as for library() or
require().
available.packages() gains a filters
argument for specifying the filtering operations performed on the
packages found in the repositories. A new built-in
"license/FOSS" filter only retains packages for which
installation can proceed solely based on packages which can be
verified as Free or Open Source Software (FOSS) employing the
available license specifications.
In registering an S3 class by a call to
setOldClass(), the data part (e.g., the object type)
required for the class can be included as one of the superclasses
in the Classes argument.
The argument f to showMethods() can be an
expression evaluating to a generic function, allowing methods to
be shown for non-exported generics and other nonstandard cases.
sprintf() now supports %o for octal
conversions.
New function Sys.readlink() for information about symbolic
links, including if a file is a symbolic link.
Package tools has new functions
checkRdaFiles() and resaveRdaFiles() to report on
the format of ‘.rda’/‘.RData’ data files, and to
re-save them in a different compressed format, including choosing
the most compact format available.
A new INSTALL option, --resave-data, makes use
of this.
File ‘~/.R/config’ is used in preference to ‘~/.Rconfig’, and these are now documented in ‘R Installation and Administration’.
Logic operations with complex numbers now work, as they were always documented to, and as in S.
arrows() and segments() allow one of x1
or y1 to be omitted to simplify the specification of
vertical or horizontal lines (suggestion of Tim Hesterberg).
approxfun() is faster by avoiding repeated NA
checks (diagnosis and patch by Karline Soetaert & Thomas
Petzoldt).
There are the beginnings of a Nynorsk translation by Karl Ove Hufthammer.
stripchart() allows par bg to be
passed in for the background colour for pch = 21 (wish of
PR#13984).
New generic function .DollarNames() to enable class authors
to customize completion after the $ extractor.
load(), save(), dput() and
dump() now open a not-yet-open connection in the
appropriate mode (as other functions using connections directly
already did).
A different regular expression engine is used for basic and extended regexps and is also for approximate matching. This is based on the TRE library of Ville Laurikari, a modified copy of which is included in the R sources.
This is often faster, especially in a MBCS locale.
Some known differences are that it is less tolerant of invalid
inputs in MBCS locales, and in its interpretation of undefined
(extended) regexps such as "^*". Also, the interpretation of
ranges such as [W-z] in caseless matching is no longer to map
the range to lower case.
This engine may in future be used in ‘literal’ mode for
fixed = TRUE, and there is a compile-time option in
src/main/grep.c to do so.
The use of repeated boundary regexps in gsub() and
gregexpr() as warned about in the help page does not work
in this engine (it did in the previous one since 2005).
Extended (and basic) regexps now support same set of options
as for fixed = TRUE and perl = TRUE, including
useBytes and support for UTF-8-encoded strings in
non-UTF-8 locales.
agrep() now has full support for MBCS locales with a modest
speed penalty. This enables help.search() to use approximate
matching character-wise rather than byte-wise.
[g]sub use a single-pass algorithm instead of
matching twice and so is usually faster.
The perl = TRUE versions now work correctly in a
non-UTF-8 MBCS locale, by translating the inputs to UTF-8.
useBytes = TRUE now inhibits the translation of inputs with
marked encodings.
strsplit() gains a useBytes argument.
The algorithm used by strsplit() has been reordered
to batch by elements of split: this can be much faster for
fixed = FALSE (as multiple compilation of regexps is avoided).
The help pages, including ?regexp, have been updated
and should be consulted for details of the new implementations.
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.
help.start() no longer sets options(htmlhelp =
TRUE) (it used to on Unix but not on Windows). Nor does it on
Unix reset the "browser" option if given an argument of
that name.
Arguments update and remote are now available
on all platforms: the default is update = FALSE since the
http server will update the package index at first use.
help() has a new argument help_type (with
default set by the option of that name) to supersede arguments
offline, htmlhelp and chmhelp
(although for now they still work if help_type is
unset). There is a new type, "PDF" to allow offline PDF
(rather than PostScript).
A function offline_help_helper() will be used if this exists
in the workspace or further down the search path, otherwise
the function of that name in the utils namespace is used.
Plain text help is now used as the fallback for HTML help (as it always was for Compiled HTML help on Windows).
It is possible to ask for static HTML pages to be prebuilt via the configure option --enable-prebuilt-html. This may be useful for those who wish to make HTML help available outside R, e.g. on a local web site.
An experimental tag \Sexpr has been added to Rd
files, to evaluate expressions at build, install, or render time.
Currently install time and render time evaluation are supported.
Tags \if, \ifelse and \out have been
added to allow format-specific (or more general, using
\Sexpr) conditional text in man pages.
The parse_Rd() parser has been made more tolerant of coding
errors in Rd files: now all syntax errors are reported as
warnings, and an attempt is made to continue parsing.
parse_Rd() now has an argument fragment
(default FALSE) to accept small fragments of Rd files (so
that \Sexpr can output Rd code which is then parsed).
parse_Rd() now always converts its input to UTF-8.
The Rd2* rendering functions have a new argument,
outputEncoding, which controls how their output is
encoded.
parse_Rd() no longer includes the newline as part of
a "%"-style comment.
There have been various bug fixes and code reorganization in
the Rd renderers Rd2HTML, Rd2latex, Rd2txt,
and Rd2ex.
All example files are now created with either ASCII or UTF-8 encoding, and the encoding is only marked in the file if there is any non-UTF-8 code (previously it was marked if the help file had non-ASCII contents, possibly in other sections).
print.Rd() now adds necessary escape characters so that
printing and re-parsing an Rd object should produce an
equivalent object.
parse_Rd() was incorrectly handling multiple backslashes in
R code strings, converting 4n+3 backslashes to 2n+1 instead
of 2n+2.
parse_Rd() now recognizes the \var tag within
a quoted string in R-like text.
parse_Rd() now treats the argument of
\command as LaTeX-like, rather than verbatim.
New function untar() to list or unpack tar archives,
possibly compressed. This uses either an external tar
command or an internal implementation.
New function tar() to create (possibly compressed)
tar archives.
New functions memCompress() and
memDecompress() for in-memory compression and
decompression.
bzfile() has a compress argument to select
the amount of effort put into compression when writing.
New function xzfile() for use with
xz-compressed files. (This can also read files
compressed by some versions of lzma.)
gzfile() looks at the file header and so can now also
read bzip2-ed files and xz-compressed files.
There are the new options of save(compress = "bzip2")
and "xz" to use bzip2 or xz
compression (which will be slower, but can give substantially
smaller files). Argument compression_level gives finer
control over the space/time tradeoffs.
load() can read such saves (but only as from this version of R).
R CMD INSTALL/check and
tools::writePACKAGES accept a wider range of compressed
tar archives. Precisely how wide depends on the capabilities of
the host 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.
R CMD INSTALL has a new option
--data-compress to control the compression used when
lazy-loading data. New possibilities are
--data-compress=bzip2 which will give ca 15% better
compression at the expense of slower installation times, and
--data-compress=xz, often giving even better compression
on large datasets at the expense of much longer installation
times. (The latter is used for the recommended packages: it is
particularly effective for survival.)
file() for open = "", "r" or
"rt" will automagically detect compressed files (from
gzip, bzip2 or xz). This means
that compressed files can be specified by file name (rather than
via a gzfile() connection) to read.table(),
readlines(), scan() and so on.
data() can handle compressed text files with extensions
‘.{txt,tab,csv}.{gz,bz2,xz}’ .
png(type="cairo1") is defunct: the value is no longer
recognized.
tools::Rd_parse() is defunct (as this version of R
uses only Rd version 2).
Use of file ‘~/.Rconf’ (which was deprecated in favour of ‘~/.Rconfig’ in 2004) has finally been removed.
Bundles of packages are deprecated. See ‘Writing R Extensions’ for the steps needed to unbundle a bundle.
help() arguments offline, htmlhelp and
chmhelp are deprecated in favour of help_type.
clearNames() (in package stats) is deprecated
for unname().
Basic regular expressions (extended = FALSE) are
deprecated in strsplit, grep and friends. There is
a precise POSIX standard for them, but it is not what recent RE
engines implement, and it seems that in almost all cases package
authors intended fixed = TRUE when using extended =
FALSE.
methods::trySilent() is deprecated in favour of
try(silent=TRUE) or – more efficiently and flexibly –
something like tryCatch(error = function(e) e).
index.search() is deprecated: there are no longer
directories of types other than help.
cairo >= 1.2 is now required (1.2.0 was released in July 2006) for cairo-based graphics devices (which remain optional).
A suitable iconv() is now required: support for
configure option --without-iconv has been withdrawn (it
was deprecated in R 2.5.0).
Perl is no longer ‘essential’. R can be built
without it, but scripts R CMD build, check,
Rprof and Sd2d currently require it.
A system glob function is now essential (a working
Sys.glob() has been assumed since R 2.9.0 at least).
C99 support for MBCS is now required, and configure option --disable-mbcs has been withdrawn.
Having a version of tar capable of automagically
detecting compressed archives is useful for
utils::untar(), and so gtar (a common name for
GNU tar) is preferred to tar: set environment
variable TAR to specify a particular tar command.
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’.
Assigning an extra 0-length column to a data frame by
DF[, "foo"] <- value now works in most cases (by filling
with NAs) or fails. (It used to give a corrupt data
frame.)
validObject() avoids an error during evaluation in the case
of various incorrect slot definitions.
n:m now returns a result of type "integer" in
a few more boundary cases.
The zap.ind argument to printCoefmat() did
not usually work as other code attempted to ensure that non-zero
values had a non-zero representation.
printCoefmat() formatted groups of columns together,
not just the cs.ind group but also the zap.ind
group and a residual group. It now formats all columns except
the cs.ind group separately (and zaps the zap.ind
group column-by-column). The main effect will be see in the
output from print.anova(), as this grouped SS-like columns
in the zap.ind group.
R_ReplDLLinit() initializes the top-level jump so
that some embedded applications on Windows no longer crash on
error.
identical() failed to take the encoding of character
strings into account, so identical byte patterns are not
necessarily identical strings, and similarly Latin-1 and UTF-8
versions of the same string differ in byte pattern.
methods(f) used to warn unnecessarily for an S4
generic f which had been created based on an existing S3
generic.
The check for consistent ordering of superclasses was not
ignoring all conditional relations (the symptom was usually
spurious warnings for classes extending "array").
Trying to assign into a raw vector with an index vector
containing NAs could cause a segfault. Reported by Hervé
Pagès.
Rscript could segfault if (by user error) its
filename argument was missing. Reported by Martin Morgan.
getAnywhere() (and functions that use it, including argument
completion in the console) did not handle special built-in
functions. Reported by Romain Francois.
order() was missing a PROTECT() call and so
could segfault when called on character data under certain (rare)
circumstances involving marked non-native encodings.
prettyNum(z, drop0trailing=TRUE) did not work
correctly when z was a complex vector. Consequently,
str(z, ...) also did not. (PR#13985)
make distclean removed too many files in
etc/ if builddir = srcdir.
R CMD replaced TEXINPUTS rather than
appending to it (as documented and intended).
help.start() no longer fails on unix when
"browser" is a function.
pbeta(x, ..., log.p = TRUE) is sometimes more accurate,
e.g., for very small x.
Unserializing a pre-2.8 workspace containing pure ASCII
character objects with a Latin-1 or UTF-8 encoding would corrupt
the CHARSXP cache.