CHANGES IN R 3.2.2| NEWS | R Documentation |
CHANGES IN R 3.2.2 It is now easier to use secure downloads from
https:// URLs on builds which support them: no longer do
non-default options need to be selected to do so. In particular,
packages can be installed from repositories which offer
https:// URLs, and those listed by setRepositories()
now do so (for some of their mirrors).
Support for https:// URLs is available on Windows, and on
other platforms if support for libcurl was compiled in and
if that supports the https protocol (system installations
can be expected to do). So https:// support can be
expected except on rather old OSes (an example being OS X
‘Snow Leopard’, where a non-system version of
libcurl can be used).
(Windows only) The default method for accessing URLs via
download.file() and url() has been changed to be
"wininet" using Windows API calls. This changes the way
proxies need to be set and security settings made: there have been
some reports of sites being inaccessible under the new default
method (but the previous methods remain available).
cmdscale() gets new option list. for increased
flexibility when a list should be returned.
configure now supports texinfo version 6.0,
which (unlike the change from 4.x to 5.0) is a minor update.
(Wish of PR#16456.)
(Non-Windows only) download.file() with default
method = "auto" now chooses "libcurl" if that is
available and a https:// or ftps:// URL is used.
(Windows only) setInternet2(TRUE) is now the default.
The command-line option --internet2 and environment
variable R_WIN_INTERNET2 are now ignored.
Thus by default the "internal" method for
download.file() and url() uses the "wininet"
method: to revert to the previous default use
setInternet2(FALSE).
This means that https:// can be read by default by
download.file() (they have been readable by file() and
url() since R 3.2.0).
There are implications for how proxies need to be set (see
?download.file): also, cacheOK = FALSE is not
supported.
chooseCRANmirror() and chooseBioCmirror() now
offer HTTPS mirrors in preference to HTTP mirrors. This changes
the interpretation of their ind arguments: see their help
pages.
capture.output() gets optional arguments type
and split to pass to sink(), and hence can be used to
capture messages.
Header ‘Rconfig.h’ now defines HAVE_ALLOCA_H if
the platform has the ‘alloca.h’ header (it is needed to
define alloca on Solaris and AIX, at least: see
‘Writing R Extensions’ for how to use it).
The libtool script generated by
configure has been modified to support FreeBSD >= 10
(PR#16410).
The HTML help page links to demo code failed due to a change in R 3.2.0. (PR#16432)
If the na.action argument was used in
model.frame(), the original data could be
modified. (PR#16436)
getGraphicsEvent() could cause a crash if a graphics
window was closed while it was in use. (PR#16438)
matrix(x, nr, nc, byrow = TRUE) failed if x
was an object of type "expression".
strptime() could overflow the allocated storage on
the C stack when the timezone had a non-standard format much
longer than the standard formats. (Part of PR#16328.)
options(OutDec = s) now signals a warning (which will
become an error in the future) when s is not a string with
exactly one character, as that has been a documented requirement.
prettyNum() gains a new option input.d.mark
which together with other changes, e.g., the default for
decimal.mark, fixes some format()ting variants with
non-default getOption("OutDec") such as in PR#16411.
download.packages() failed for type equal to
either "both" or "binary". (Reported by Dan
Tenenbaum.)
The dendrogram method of labels() is much more
efficient for large dendrograms, now using rapply().
(Comment #15 of PR#15215)
The "port" algorithm of nls() could give
spurious errors. (Reported by Radford Neal.)
Reference classes that inherited from reference classes in
another package could invalidate methods of the inherited
class. Fixing this requires adding the ability for methods to be
“external”, with the object supplied explicitly as the first
argument, named .self. See "Inter-Package Superclasses"
in the documentation.
readBin() could fail on the SPARC architecture
due to alignment issues. (Reported by Radford Neal.)
qt(*, df=Inf, ncp=.) now uses the natural
qnorm() limit instead of returning NaN. (PR#16475)
Auto-printing of S3 and S4 values now searches for
print() in the base namespace and show() in the
methods namespace instead of searching the global
environment.
polym() gains a coefs = NULL argument and
returns class "poly" just like poly() which gets a
new simple=FALSE option. They now lead to correct
predict()ions, e.g., on subsets of the original data.
rhyper(nn, <large>) now works correctly. (PR#16489)
ttkimage() did not (and could not) work so was
removed. Ditto for tkimage.cget() and
tkimage.configure(). Added two Ttk widgets and missing
subcommands for Tk's image command:
ttkscale(),
ttkspinbox(),
tkimage.delete(),
tkimage.height(),
tkimage.inuse(),
tkimage.type(),
tkimage.types(),
tkimage.width(). (PR#15372, PR#16450)
getClass("foo") now also returns a class definition when it is
found in the cache more than once.
CHANGES IN R 3.2.1utf8ToInt() now checks that its input is valid UTF-8
and returns NA if it is not.
install.packages() now allows type = "both"
with repos = NULL if it can infer the type of file.
nchar(x, *) and nzchar(x) gain a new argument
keepNA which governs how the result for NAs in
x is determined. For the R 3.2.x series, the default
remains FALSE which is fully back compatible.
From R 3.3.0, the default will change to keepNA = NA and
you are advised to consider this for code portability.
news() more flexibly extracts dates from package
‘NEWS.Rd’ files.
lengths(x) now also works (trivially) for atomic
x and hence can be used more generally as an efficient
replacement of sapply(x, length) and similar.
The included version of PCRE has been updated to 8.37, a bug-fix release.
diag() no longer duplicates a matrix when extracting
its diagonal.
as.character.srcref() gains an argument to allow
characters corresponding to a range of source references to be
extracted.
acf() and ccf() now guarantee values strictly
in [-1,1] (instead of sometimes very slightly outside). PR#15832.
as.integer("111111111111") now gives NA (with a warning) as
it does for the corresponding numeric or negative number
coercions. Further, as.integer(M + 0.1) now gives M
(instead of NA) when M is the maximal representable integer.
On some platforms nchar(x, "c") and nchar(x, "w")
would return values (possibly NA) for inputs which were
declared to be UTF-8 but were not, or for invalid strings without a
marked encoding in a multi-byte locale, rather than give an
error. Additional checks have been added to mitigate this.
apply(a, M, function(u) c(X = ., Y = .)) again
has dimnames containing "X" and "Y" (as in R < 3.2.0).
(Windows only) In some cases, the --clean option
to R CMD INSTALL could fail. (PR#16178)
(Windows only) choose.files() would occasionally
include characters from the result of an earlier call in
the result of a later one. (PR#16270)
A change in RSiteSearch() in R 3.2.0 caused it to
submit invalid URLs. (PR#16329)
Rscript and command line R silently
ignored incomplete statements at the end of a script; now they
are reported as parse errors. (PR#16350)
Parse data for very long strings was not stored. (PR#16354)
plotNode(), the workhorse of the plot method
for "dendrogram"s is no longer recursive, thanks to Suharto
Anggono, and hence also works for deeply nested dendrograms. (PR#15215)
The parser could overflow internally when given numbers in scientific format with extremely large exponents. (PR#16358)
If the CRAN mirror was not set, install.packages(type = "both")
and related functions could repeatedly query the user for it.
(Part of PR#16362)
The low-level functions .rowSums() etc. did not
check the length of their argument, so could segfault. (PR#16367)
The quietly argument of library() is now
correctly propagated from .getRequiredPackages2().
Under some circumstances using the internal PCRE when
building R from source would cause external libs such as
-llzma to be omitted from the main link.
The .Primitive default methods of the logic operators, i.e.,
!, & and |, now give correct error messages
when appropriate, e.g., for `&`(TRUE) or `!`().
(PR#16385)
cummax(x) now correctly propagates NAs also
when x is of type integer and begins with an NA.
summaryRprof() could fail when the profile contained
only two records. (PR#16395)
HTML vignettes opened using vignette() did not support
links into the rest of the HTML help system. (Links worked properly
when the vignette was opened using browseVignettes() or from
within the help system.)
arima(*, xreg = .) (for d >= 1)
computes estimated variances based on a the number of effective
observations as in R version 3.0.1 and earlier. (PR#16278)
slotNames(.) is now correct for "signature"
objects (mostly used internally in methods).
On some systems, the first string comparison after
a locale change would result in NA.
CHANGES IN R 3.2.0anyNA() gains a recursive argument.
When x is missing and names is not false
(including the default value), Sys.getenv(x, names) returns
an object of class "Dlist" and hence prints tidily.
(Windows.) shell() no longer consults the
environment variable SHELL: too many systems have been
encountered where it was set incorrectly (usually to a path where
software was compiled, not where it was installed).
R_SHELL, the preferred way to select a non-default shell,
can be used instead.
Some unusual arguments to embedFonts() can now be
specified as character vectors, and the defaults have been changed
accordingly.
Functions in the Summary group duplicate less.
(PR#15798)
(Unix-alikes.) system(cmd, input = ) now uses
‘shell-execution-environment’ redirection, which will be
more natural if cmd is not a single command (but requires a
POSIX-compliant shell). (Wish of PR#15508)
read.fwf() and read.DIF() gain a
fileEncoding argument, for convenience.
Graphics devices can add attributes to their description in
.Device and .Devices. Several of those included with
R use a "filepath" attribute.
pmatch() uses hashing in more cases and so is faster
at the expense of using more memory. (PR#15697)
pairs() gains new arguments to select sets of
variables to be plotted against each other.
file.info(, extra_cols = FALSE) allows a minimal set
of columns to be computed on Unix-alikes: on some systems without
properly-configured caching this can be significantly faster with
large file lists.
New function dir.exists() in package base to
test efficiently whether one or more paths exist and are
directories.
dput() and friends gain new controls
hexNumeric and digits17 which output double and
complex quantities as, respectively, binary fractions (exactly,
see sprintf("%a")) and as decimals with up to 17
significant digits.
save(), saveRDS() and serialize() now
support ascii = NA which writes ASCII files using
sprintf("%a") for double/complex quantities. This is
read-compatible with ascii = TRUE but avoids
binary->decimal->binary conversions with potential loss of
precision. Unfortunately the Windows C runtime's lack of C99
compliance means that the format cannot be read correctly there in
R before 3.1.2.
The default for formatC(decimal.mark =) has been
changed to be getOption("OutDec"); this makes it more
consistent with format() and suitable for use in print
methods, e.g. those for classes "density", "ecdf",
"stepfun" and "summary.lm".
getOption("OutDec") is now consulted by the print method
for class "kmeans", by cut(), dendrogram(),
plot.ts() and quantile() when constructing labels
and for the report from legend(trace = TRUE).
(In part, wish of PR#15819.)
printNum() and hence format() and
formatC() give a warning if big.mark and
decimal.mark are set to the same value (period and comma
are not uncommonly used for each, and this is a check that
conventions have not got mixed).
merge() can create a result which uses long vectors
on 64-bit platforms.
dget() gains a new argument keep.source which
defaults to FALSE for speed (dput() and
dget() are most often used for data objects where this can
make dget() many times faster).
Packages may now use a file of common macro definitions in their help files, and may import definitions from other packages.
A number of macros have been added in the new
‘share/Rd’ directory for use in package overview help pages,
and promptPackage() now makes use of them.
tools::parse_Rd() gains a new permissive
argument which converts unrecognized macros into text. This is
used by utils:::format.bibentry to allow LaTeX markup to be
ignored.
options(OutDec =) can now specify a multi-byte
character, e.g., options(OutDec = "\u00b7") in a UTF-8
locale.
is.recursive(x) is no longer true when x is an
external pointer, a weak reference or byte code; the first enables
all.equal(x, x) when x <- getClass(.).
ls() (aka objects()) and
as.list.environment() gain a new argument sorted.
The "source" attribute (which has not been added to
functions by R since before R version 2.14.0) is no longer
treated as special.
Function returnValue() has been added to give
on.exit() code access to a function's return value for
debugging purposes.
crossprod(x, y) allows more matrix coercions when
x or y are vectors, now equalling
t(x) %*% y in these cases (also reported by Radford Neal).
Similarly, tcrossprod(x,y) and %*% work in more
cases with vector arguments.
Utility function dynGet() useful for detecting
cycles, aka infinite recursions.
The byte-code compiler and interpreter include new instructions that allow many scalar subsetting and assignment and scalar arithmetic operations to be handled more efficiently. This can result in significant performance improvements in scalar numerical code.
apply(m, 2, identity) is now the same as the matrix
m when it has named row names.
A new function debuggingState() has been added,
allowing to temporarily turn off debugging.
example() gets a new optional argument
run.donttest and tools::Rd2ex() a corresponding
commentDonttest, with a default such that
example(..) in help examples will run \donttest
code only if used interactively (a change in behaviour).
rbind.data.frame() gains an optional argument
make.row.names, for potential speedup.
New function extSoftVersion() to report on the
versions of third-party software in use in this session.
Currently reports versions of zlib, bzlib, the
liblzma from xz, PCRE, ICU, TRE and the iconv
implementation.
A similar function grSoftVersion() in package grDevices
reports on third-party graphics software.
Function tcltk::tclVersion() reports the Tcl/Tk version.
Calling callGeneric() without arguments now works
with primitive generics to some extent.
vapply(x, FUN, FUN.VALUE) is more efficient notably
for large length(FUN.VALUE); as extension of PR#16061.
as.table() now allows tables with one or more
dimensions of length 0 (such as as.table(integer())).
names(x) <- NULL now clears the names of call
and ... objects.
library() will report a warning when an insufficient
dependency version is masking a sufficient one later on the
library search path.
A new plot() method for class "raster" has
been added.
New check_packages_in_dir_changes() function in
package tools for conveniently analyzing how changing
sources impacts the check results of their reverse dependencies.
Speed-up from Peter Haverty for ls() and
methods:::.requirePackage() speeding up package loading.
(PR#16133)
New get0() function, combining exists() and
get() in one call, for efficiency.
match.call() gains an envir argument for
specifying the environment from which to retrieve
the ... in the call, if any; this environment was wrong
(or at least undesirable) when the definition argument was
a function.
topenv() has been made .Internal() for
speedup, based on Peter Haverty's proposal in PR#16140.
getOption() no longer calls options() in the main
case.
Optional use of libcurl (version 7.28.0 from Oct 2012
or later) for Internet access:
capabilities("libcurl") reports if this is
available.
libcurlVersion() reports the version in use, and
other details of the "libcurl" build including which URL
schemes it supports.
curlGetHeaders() retrieves the headers for
http://, https://, ftp:// and
ftps:// URLs: analysis of these headers can provide
insights into the ‘existence’ of a URL (it might for example be
permanently redirected) and is so used in R CMD
check --as-cran.
download.file() has a new optional method
"libcurl" which will handle more URL schemes, follow
redirections, and allows simultaneous downloads of multiple
URLs.
url() has a new method "libcurl" which
handles more URL schemes and follows redirections. The default
method is controlled by a new option url.method, which
applies also to the opening of URLs via file()
(which happens implicitly in functions such as
read.table.)
When file() or url() is invoked with a
https:// or ftps:// URL which the current method
cannot handle, it switches to a suitable method if one is
available.
(Windows.) The DLLs ‘internet.dll’ and ‘internet2.dll’ have been merged. In this version it is safe to switch (repeatedly) between the internal and Windows internet functions within an R session.
The Windows internet functions are still selected by flag
--internet2 or setInternet2(). This can be
overridden for an url() connection via its new
method argument.
download.file() has new method "wininet", selected
as the default by --internet2 or setInternet2().
parent.env<- can no longer modify the parent of a
locked namespace or namespace imports environment. Contributed by
Karl Millar.
New function isNamespaceLoaded() for readability and speed.
names(env) now returns all the object names of an
environment env, equivalently to
ls(env, all.names = TRUE, sorted = FALSE) and also to
the names of the corresponding list,
names(as.list(env, all.names = TRUE)).
Note that although names() returns a character vector, the
names have no particular ordering.
The memory manager now grows the heap more aggressively. This reduces the number of garbage collections, in particular while data or code are loaded, at the expense of slightly increasing the memory footprint.
New function trimws() for removing leading/trailing
whitespace.
cbind() and rbind() now consider S4 inheritance
during S3 dispatch and also obey deparse.level.
cbind() and rbind() will delegate recursively
to methods::cbind2 (methods::rbind2) when at least
one argument is an S4 object and S3 dispatch fails (due to
ambiguity).
(Windows.) download.file(quiet = FALSE) now uses
text rather than Windows progress bars in non-interactive use.
New function hsearch_db() in package utils for
building and retrieving the help search database used by
help.search(), along with functions for inspecting the
concepts and keywords in the help search database.
New function .getNamespaceInfo(), a no-check version
of getNamespaceInfo() mostly for internal speedups.
The help search system now takes \keyword entries in Rd files which are not standard keywords (as given in ‘KEYWORDS’ in the R documentation directory) as concepts. For standard keyword entries the corresponding descriptions are additionally taken as concepts.
New lengths() function for getting the lengths of all
elements in a list.
New function toTitleCase() in package tools,
tailored to package titles.
The matrix methods of cbind() and rbind()
allow matrices as inputs which have 2^31 or more
elements. (For cbind(), wish of PR#16198.)
The default method of image() has an explicit check
for a numeric or logical matrix (which was always required).
URLencode() will not by default encode further URLs
which appear to be already encoded.
BIC(mod) and BIC(mod, mod2) now give non-NA
numbers for arima() fitted models, as nobs(mod) now
gives the number of “used” observations for such models.
This fixes PR#16198, quite differently than proposed there.
The print() methods for "htest",
"pairwise.htest" and "power.htest" objects now have
a digits argument defaulting to (a function of)
getOption("digits"), and influencing all printed numbers
coherently. Unavoidably, this changes the display of such test
results in some cases.
Code completion for namespaces now recognizes all loaded namespaces, rather than only the ones that are also attached.
The code completion mechanism can now be replaced by a user-specified completer function, for (temporary) situations where the usual code completion is inappropriate.
unzip() will now warn if it is able to detect truncation
when unpacking a file of 4GB or more (related to PR#16243).
methods() reports S4 in addition to S3 methods;
output is simplified when the class argument is
used. .S3methods() and methods::.S4methods() report
S3 and S4 methods separately.
Higher order functions such as the apply functions
and Reduce() now force arguments to the functions they apply
in order to eliminate undesirable interactions between lazy
evaluation and variable capture in closures. This resolves
PR#16093.
The \donttest sections of R's help files can be
tested by
make check TEST_DONTTEST=TRUE .
It is possible to request the use of system
valgrind headers via configure option
--with-system-valgrind-headers: note the possible future
incompatibility of such headers discussed in the 'R Installation
and Administration' manual. (Wish of PR#16068.)
The included version of liblzma has been updated to
xz-utils 5.0.7 (minor bug fixes from 5.0.5).
configure options --with-system-zlib,
--with-system-bzlib and --with-system-pcre are
now the default. For the time being there is fallback to the
versions included in the R sources if no system versions are
found or (unlikely) if they are too old.
Linux users should check that the -devel or -dev
versions of packages zlib, bzip2/libbz2 and
pcre as well as xz-devel/liblzma-dev (or
similar names) are installed.
configure by default looks for the
texi2any script from texinfo 5.1 or later, rather
than the makeinfo program. (makeinfo is a
link to the Perl script texi2any in texinfo 5.x.)
R CMD INSTALL gains an option
--built-timestamp=STAMP allowing 100% reproducible
package building, thanks to Dirk Eddelbuettel.
There is support for testing the \dontrun and
\donttest parts of examples in packages.
tools::testInstalledPackage() accepts new arguments
commentDontrun = FALSE and commentDonttest = FALSE.
R CMD check gains options --run-dontrun and
--run-donttest.
The HTML generated by tools::Rd2HTML() and
tools::toHTML() methods is now
‘XHTML 1.0 Strict’.
The compiler package's utility function
setCompilerOptions() now returns the old values
invisibly. The initial optimization level can also be set with the
environment variable R_COMPILER_OPTIMIZE.
R CMD build adds a NeedsCompilation field
if one is not already present in the ‘DESCRIPTION’ file.
R CMD check gains option --test-dir to
specify an alternative set of tests to run.
R CMD check will now by default continue with
testing after many types of errors, and will output a summary
count of errors at the end if any have occurred.
R CMD check now checks that the Title and
Description fields are correctly terminated.
R CMD check --as-cran now:
checks a ‘README.md’ file can be processed: this
needs pandoc installed.
checks the existence and accessibility of URLs in the
‘DESCRIPTION’, ‘CITATION’, ‘NEWS.Rd’ and
‘README.md’ files and in the help files (provided the build
has libcurl support).
reports non-ASCII characters in R source files when there is no package encoding declared in the ‘DESCRIPTION’ file.
reports (apparent) S3 methods exported but not registered.
reports overwriting registered S3 methods from base/recommended packages. (Such methods are replaced in the affected package for the rest of the session, even if the replacing namespace is unloaded.)
reports if the Title field does not appear to be in
title case (see ‘Writing R Extensions’: there may be
false positives, but note that technical words should be
single-quoted and will then be accepted).
Most of these checks can also be selected by environment variables: see the ‘R Internals’ manual.
New C API utility logspace_sum(logx[], n).
Entry points rbinom_mu, rnbinom_mu and
rmultinom are remapped (by default) to Rf_rbinom_mu
etc. This requires packages using them to be re-installed.
.C(DUP = FALSE) and .Fortran(DUP = FALSE) are
now ignored, so arguments are duplicated if DUP = TRUE
would do so. As their help has long said, .Call() is much
preferred.
New entry point R_allocLD, like R_alloc but
guaranteed to have sufficient alignment for long double
pointers.
isPairList() now returns TRUE for DOTSXP.
A number of changes to the Windows build system are in development. The following are currently in place.
Installation using external binary distributions of zlib, bzip2, liblzma, pcre, libpng, jpeglib and libtiff is now required, and the build instructions have been revised.
A new make target rsync-extsoft has been
added to obtain copies of the external libraries from
CRAN.
Building the manuals now requires texi2any from
texinfo 5.1 or later. CRAN binary builds include
the manuals, but by default builds from source will not, and they
will be accessed from CRAN. See the comments in
‘src/gnuwin32/MkRules.dist’ for how to specify the location
of texi2any.
(Windows) Changes have been made to support an experimental Windows toolchain based on GCC 4.9.2. The default toolchain continues to be based on GCC 4.6.3, as the new toolchain is not yet stable enough. A change to a new toolchain is expected during the R 3.2.x lifetime.
(Windows) The use of macro ZLIB_LIBS in file
‘src/Makevars.win’ (which has not been documented for a long
time) now requires an external ‘libz.a’ to be available (it is
part of the ‘goodies’ used to compile Windows binary
packages). It would be simpler to use -lz instead.
The default for option pkgType on platforms using
binary packages is now "both", so source packages will be
tried if binary versions are not available or not up to date.
There are options for what install.packages(type = "both")
(possibly called via update.packages()) will do if
compilation of a source package is desirable: see ?options
(under utils).
If you intend not to accept updates as source packages, you should
use update.packages(type = "binary").
download.file(method = "lynx") is defunct.
Building R using the included versions of zlib,
bzip2, xz and PCRE is deprecated: these are frozen
(bar essential bug-fixes) and will be removed for R 3.3.0.
The configure option
--with-valgrind-instrumentation=3 has been withdrawn, as
it did not work with recent valgrind headers: it is now
treated as level 2.
The MethodsList class in package methods had
been deprecated in R 2.11.0 and is defunct now. Functions using
it are defunct if they had been deprecated in R 2.11.0, and are
deprecated now, otherwise.
Fixed two obscure bugs in pairlist subassignment, reported by Radford Neal as part of pqR issue 16.
Fixes for bugs in handling empty arguments and argument
matching by name in log().
all.equal() gains methods for environments and
refClasses.
[<- and [[<- gain S4 data.frame methods
to avoid corruption of S4 class information by the S3 methods.
callNextMethod() should now work within a .local
call when ... is absent from formals(.local).
dput(pairlist(x)) generates a call to the
pairlist constructor instead of the list
constructor.
Fix missing() when arguments are propagated through
... . (PR#15707)
eigen(m) now defaults to symmetric = TRUE even
when the dimnames are asymmetric if the matrix is otherwise
symmetric. (PR#16151)
Fix issues with forwarding ... through
callGeneric() and callNextMethod(). (PR#16141)
callGeneric() now works after a callNextMethod().
Subclass information is kept consistent when replacing an
ordinary S4 class with an “old class” via the
S4Class argument to setOldClass(). Thus, for
example, a data.frame is valid for a list argument
in the signature, and a factor is valid for vector
arguments.
In qbeta() the inversion of pbeta() is much
more sophisticated. This works better in corner cases some of
which failed completely previously (PR#15755), or were using
too many iterations.
Auto-printing no longer duplicates objects when printing is dispatched to a method.
kmeans(x, k) would fail when nrow(x) >= 42949673.
(Comment 6 of PR#15364)
‘Abbreviated’ locale-specific day and month names could have been truncated in those rare locales where there are the same as the full names.
An irrelevant warning message from updating subclass information was silenced (the namespace would not be writable in this case).
CHANGES IN R 3.1.3 The internal method of download.file() can now handle
files larger than 2GB on 32-bit builds which support such files
(tested on 32-bit R running on 64-bit Windows).
kruskal.test() warns on more types of suspicious input.
The as.dendrogram() method for "hclust"
objects gains a check argument protecting against memory
explosion for invalid inputs.
capabilities() has a new item long.double
which indicates if the build uses a long double type which
is longer than double.
nlm() no longer modifies the callback argument in
place (a new vector is allocated for each invocation, which mimics
the implicit duplication that occurred in R < 3.1.0); note that
this is a change from the previously documented
behavior. (PR#15958)
icuSetCollate() now accepts locale = "ASCII"
which uses the basic C function strcmp and so collates
strings byte-by-byte in numerical order.
sessionInfo() tries to report the OS version in use
(not just that compiled under, and including details of Linux
distributions).
model.frame() (used by lm() and many other
modelling functions) now warns when it drops contrasts
from factors. (Wish of PR#16119)
install.packages() and friends now accept the value
type = "binary" as a synonym for the native binary type on
the platform (if it has one).
Single source or binary files can be supplied for
install.packages(type = "both") and the appropriate type
and repos = NULL will be inferred.
New function pcre_config() to report on some of the
configuration options of the version of PCRE in use. In
particular, this reports if regular expressions using
\p{xx} are supported.
(Windows.) download.file(cacheOK = FALSE) is now
supported when ‘internet2.dll’ is used.
browseURL() has been updated to work with Firefox
36.0 which has dropped support for the -remote interface.
The included version of PCRE has been updated to 8.36.
configure accepts MAKEINFO=texi2any as
another way to ensure texinfo 5.x is used when both 5.x and
4.x are installed.
R CMD check now checks the packages used in
\donttest sections of the examples are specified in the
‘DESCRIPTION’ file.
(These are needed to run the examples interactively.)
R CMD check checks for the undeclared use of GNU
extensions in Makefiles, and for Makefiles with a missing final
linefeed.
R CMD build will correct line endings in all Makefiles,
not just those in the ‘src’ directory.
R CMD check notes uses of library() and
require() in package code: see the section
‘Suggested packages’ of ‘Writing R Extensions’ for
good practice.
The configure option
--with-valgrind-instrumentation=3 is deprecated and will
be removed in R 3.2.0.
(Windows.) Rscript.exe was missing a
manifest specifying the modern style for common controls (e.g.,
the download progress bar).
If a package had extra documentation files but no vignette, the HTML help system produced an empty index page.
The parser now gives an error if a null character is included in a string using Unicode escapes. (PR#16046)
qr.Q() failed on complex arguments due to
pre-3.0(!) typo. (PR#16054)
abs() failed with named arguments when the argument
was complex. (PR#16047)
"noquote" objects may now be used as columns in
dataframes. (PR#15997)
Some values with extremely long names were printed incorrectly. (PR#15999)
Extremely large exponents on zero expressed in scientific
notation (e.g. 0.0e50000) could give NaN. (PR#15976)
download.file() reported downloaded sizes as 0KB if
less than 1MB, only for R 3.1.2 and only on big-endian platforms.
prompt() did not escape percent signs in the
automatically generated usage section of help files.
drop.terms() dropped some of the attributes of the
object it was working with. (PR#16029)
(Windows.) The command completion in Rgui.exe
messed up the console. (PR#15791)
(Windows.) The choose.files() command returned a
blank string when the user asked for a single file but cancelled
the request. (PR#16074)
Math2 S4 group generics failed to correctly dispatch
"structure"- and "nonStructure"-derived classes.
loadNamespace() imposed undocumented restrictions
on the versionCheck parameter. (Reported by Geoff Lee.)
Rare over-runs detected by AddressSanitizer in
substr() and its replacement version have been avoided.
Inter alia that fix gives the documented behaviour for
substr(x, 1, 2) <- "" (subsequently reported as
PR#16214).
Loading packages incorrectly defining an S4 generic followed by a function of the same name caused an erroneous cyclic namespace dependency error.
Declared vignette encodings are now always passed to the vignette engine.
Port Tomas Kalibera's fix from R-devel that restores the
loadMethod() fast path, effectively doubling the speed of
S4 dispatch.
power.t.test() and power.prop.test() now make
use of the extendInt option of uniroot() and hence
work in more extreme cases. (PR#15792)
If a package was updated and attached when its namespace was already loaded, it could end up with parts from one version and parts from the other. (PR#16120)
tools:::.Rdconv() didn't accept --encoding= due
to a typo. (PR#16121)
Unix-alike builds without a suitable makeinfo were
documented to link the missing HTML manuals to CRAN, but did not.
save(*, ascii=TRUE) and load() now correctly
deal with NaN's. (PR#16137)
split.Date() retains fractional representations while
avoiding incomplete class propagation.
‘R_ext/Lapack.h’ had not been updated for changes made
by LAPACK to the argument lists of its (largely internal)
functions dlaed2 and dlaed3. (PR#16157)
RShowDoc("NEWS", "txt") had not been updated for the
layout changes of R 3.1.0.
The xtfrm() method for class "Surv" has been
corrected and its description expanded.
mode(x) <- y would incorrectly evaluate x before
changing its mode. (PR#16215)
besselJ(1, 2^64) and besselY(..) now signal a
warning, returning NaN instead of typically
segfaulting. (Issue 3 of PR#15554)
HTML conversion of \href markup in ‘.Rd’ files did not remove the backslash from \% and so gave an invalid URL. In a related change, the \ escape is now required in such URLs.
CHANGES IN R 3.1.2embedFonts() now defaults to
format = "ps2write" for ‘.ps’ and ‘.eps’ files.
This is available in Ghostscript 9.x (since 2010) whereas the
previous default, format = "pswrite", was removed in
Ghostscript 9.10.
For consistency with [dpqr]norm(),
[dp]lnorm(sdlog = 0) model a point mass at
exp(mulog) rather than return NaN (for an error).
capabilities() now reports if ICU is compiled in for
use for collation (it is only actually used if a suitable locale
is set for collation, and never for a C locale).
(OS X only.) Package tcltk checks when loaded if it is linked against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk component and the X11 libraries are installed. This allows more informative error messages to be given advising the installation of the missing component or of XQuartz.
The X11() device and X11-based versions of the data editor
and viewer (invoked by edit() and View() for data
frames and matrices from command-line R) check that the X11
libraries are installed and if not advises installing XQuartz.
icuSetCollate() allows locale = "default", and
locale = "none" to use OS services rather than ICU for
collation.
Environment variable R_ICU_LOCALE can be used to set the default ICU locale, in case the one derived from the OS locale is inappropriate (this is currently necessary on Windows).
New function icuGetCollate() to report on the ICU
collation locale in use (if any).
utils::URLencode() was updated to use unreserved and
reserved characters from RFC 3986
(http://tools.ietf.org/html/rfc3986) instead of RFC 1738.
unique(warnings()) and c(warnings()) are now
supported.
The Bioconductor ‘version’ used by
setRepositories() now defaults to 3.0. (It can be
set at runtime via environment variable
R_BIOC_VERSION.)
Omegahat is no longer listed as providing Windows binary
packages, e.g. by setRepositories(). It has no binary
packages available for R 3.1.x and those for earlier versions
were 32-bit only.
The configure script reports on the more important
capabilities/options which will not be compiled in.
More types of external BLAS are recognized by name in that report.
When building R as a shared library, the
-L${R_HOME}/lib${R_ARCH} flag is placed earlier in the
link commands used during installation and when packages are
installed: this helps ensure that the current build has priority
if an R shared library has already been installed by
e.g. install-libR in a library mentioned in
LDFLAGS (and not in ‘your system's library directory’
as documented). (Wish of PR#15790.)
LaTeX package upquote is no longer required for R's use of inconsolata.
(Windows only) If both 32- and 64-bit versions of R are installed, the ‘bin/R.exe’ and ‘bin/Rscript.exe’ executables now run 64-bit R. (To run 32-bit R, overwrite these files with copies of ‘bin/i386/Rfe.exe’.)
Running R CMD check with
_R_CHECK_DEPENDS_ONLY_ true now makes the
VignetteBuilder packages available even if they are
listed in Suggests, since they are needed to recognise and
process non-Sweave vignettes.
R CMD check now reports empty importFrom
declarations in a ‘NAMESPACE’ file, as these are common
errors (writing importFrom(Pkg) where
import(Pkg) was intended).
R CMD check now by default checks code usage
directly on the package namespace without loading and attaching
the package and its suggests and enhances. For good practice with
packages in the Suggests field, see §1.1.3.1 of
‘Writing R Extensions’. For use of lazy-data objects in
the package's own code, see ?data.
dmultinom() did not handle non-finite probabilities
correctly.
prettyNum(x, zero.print=*) now also works when
x contains NAs.
A longstanding bug exhibited by nlminb() on Windows
was traced to a compiler bug in gcc 4.6.3; a workaround has been
put in place. (PR#15244 and PR#15914).
Rendering of \command in HTML versions of help pages
has been improved: this is particularly evident on the help page
for INSTALL.
as.hexmode(x) and as.octmode(x) now behave
correctly for some numeric x, e.g., c(NA, 1) or
c(1, pi).
drop1() failed if the scope argument had
no variables to drop. (PR#15935)
edit() (and hence fix()) failed if
an object had a non-character attribute named "source"
(an attribute that had been used in R prior to version 2.14.0).
callGeneric() could fail if the generic had
... as a formal argument. (PR#15937).
Forking in package parallel called C entry point
exit in the child. This was unsafe (_exit should
have been called), and could flush stdin of the main R
process (seen most often on Solaris).
As good practice, stdout is now flushed before forking a child.
R objects such as list(`a\b` = 1) now print correctly.
getAnywhere("C_pbinom") now returns correctly a
single object (rather than unlisting it).
The confint() method for nls() fits failed it
these has specified parameter limits despite using an algorithm
other than "port". (PR#15960)
Subclassing an S4 class failed if the class required
arguments to the generator, through its initialize() method.
removeSource() did not properly handle expressions
containing arguments that were supplied as missing, e.g.
x[i,]. (PR#15957)
as.environment(list()) now works, and
as.list() of such an environment is now the same as
list().
Several tcltk functions failed when run in unusual environments. (PR#15970)
options(list()) now works (trivially). (PR#15979)
merge(<dendrogram>, ..) now works correctly for two
‘independent’ dendrograms (PR#15648), and still compatibly via
adjust = "auto" e.g. for two branches of an existing
dendrogram.
The plot method for "hclust" objects gets an
optional argument check; when that is true (the default) it
checks more carefully for valid input.
(Windows only) If a user chose to install 64 bit R but not 32 bit R, the ‘bin/R’ and ‘bin/Rscript’ executables failed to run. (PR#15981)
Various possible buffer overruns have been prevented, and missed memory protection added. (PR#15990)
Rscript no longer passes --args to
R when there are no extra (“user”) arguments.
objects like getClass("refClass")@prototype now
print() and str() without error.
identical() now also looks at the S4 bit.
hist(x, breaks) is more robust in adding a small fuzz
to few breaks when some are very large. (PR#15988)
sub() and gsub() did not handle regular
expressions like "\s{2,}" properly if the text
contained NA or non-ascii elements in a UTF-8
locale. Part of this was due to a bug in the TRE library.
(PR#16009)
RShowDoc("NEWS") now displays the PDF version.
Matrices and arrays with last dimension zero did not print at all or incompletely. (PR#16012)
plot.histogram() and hence hist() now respect
the xaxs, yaxs and lab graphics parameters.
(PR#16021)
bw.SJ(x) and other bw.*() no longer segfault when
x contains non-finite values. (PR#16024)
R CMD Rd2pdf unintentionally ignored its
--os option.
The internal method of download.file() was not
reporting file sizes and progress correctly on files larger than
2GB (inherited from libxml2). This is corrected for 64-bit
builds (32-bit platforms may not support such files, but where
possible will be supported in future versions of R).
Work around a bug in OS X Yosemite where key environment variables may be duplicated causing issues in subprocesses. The duplicates are now removed on R startup (via Rprofile). (PR#16042)
Adjust X11 auto-launch detection in DISPLAY on OS X to recognize latest XQuartz.
CHANGES IN R 3.1.1 When attach() reports conflicts, it does so
compatibly with library() by using message().
R CMD Sweave no longer cleans any files by
default, compatibly with versions of R prior to 3.1.0. There are
new options --clean, --clean=default and
--clean=keepOuts.
tools::buildVignette() and tools::buildVignettes()
with clean = FALSE no longer remove any created files.
buildvignette() gains a keep argument for more
cleaning customization.
The Bioconductor ‘version’ used by
setRepositories() can now be set by environment variable
R_BIOC_VERSION at runtime, not just when R is installed.
(It has been stated that Bioconductor will switch from
‘version’ 2.14 to ‘version’ 3.0 during the lifetime
of the R 3.1 series.)
Error messages from bugs in embedded Sexpr code in Sweave documents now report the source location.
type.convert(), read.table() and similar
read.*() functions get a new numerals argument,
specifying how numeric input is converted when its conversion to
double precision loses accuracy. The default value,
"allow.loss" allows accuracy loss, as in R versions before
3.1.0.
For some compilers, integer addition could overflow without a warning. R's internal code for both integer addition and subtraction is more robust now. (PR#15774)
The function determining the default number of knots for
smooth.spline() is now exported, as .nknots.smspl().
dbeta(, a,b), pbeta(), qbeta() and
rbeta() are now defined also for a = 0, b = 0,
or infinite a and b (where they typically returned
NaN before).
Many package authors report that the RStudio graphics device
does not work correctly with their package's use of
dev.new(). The new option dev.new(noRStudioGD =
TRUE) replaces the RStudio override by the default device as
selected by R itself, still respecting environment variables
R_INTERACTIVE_DEVICE and R_DEFAULT_DEVICE.
readRDS() now returns visibly.
Modifying internal logical scalar constants now results in an error instead of a warning.
install.packages(repos = NULL) now accepts
http:// or ftp:// URLs of package archives as well
as file paths, and will download as required. In most cases
repos = NULL can be deduced from the extension of the URL.
The warning when using partial matching with the $
operator on data frames is now only given when
options("warnPartialMatchDollar") is TRUE.
Package help requests like package?foo now
try the package foo whether loaded or not.
General help requests now default to trying all loaded packages, not just those on the search path.
Added a new function promptImport(), to generate a
help page for a function that was imported from another package
(and presumably re-exported, or help would not be needed).
configure option --with-internal-tzcode
can now be used with variable rsharedir.
The included version of PCRE has been updated to 8.35.
There is a new target make uninstall-libR to
remove an installed shared/static ‘libR’.
make install-libR now works if a sub-architecture is
used, although the user will need to specify libdir
differently for different sub-architectures.
There is more extensive advice on which LaTeX packages are
required to install R or to make package manuals (as done by
R CMD check) in the ‘Writing R Extensions’
manual.
Compilers/linkers were handling the visibility control in ‘src/extra/xz’ inconsistently (and apparently in some cases incorrectly), so it has been simplified. (PR#15327)
(Windows) There is updated support for the use of ICU for collation: see the ‘R Installation and Administration Manual’.
dbinom(x, n), pbinom(), dpois(), etc,
are slightly less restrictive in checking if n is
integer-valued. (Wish of PR#15734.)
pchisq(x, df, ncp, log.p = TRUE) is more accurate and
no longer underflows for small x and ncp < 80, e.g,
for pchisq(1e-5, df = 100, ncp = 1, log = TRUE).
(Based on PR#15635 and a suggestion by Roby Joehanes.)
The s (“step into”) command in the debugger
would cause R to step into expressions evaluated there,
not just into functions being debugged. (PR#15770)
The C code used by strptime() rejected time-zone
offsets of more than +1200 (+1245, +1300 and
+1400 can occur). (PR#15768)
(Windows only.)
png(type = "cairo", antialias = "gray")
was not accepted. (PR#15760)
Use of save(..., envir=) with named objects could
fail. (PR#15758)
Sweave() mis-parsed Sexpr expressions that
contained backslashes. (PR#15779)
The return value from options(foo = NULL) was not
the previous value of the option. (PR#15781)
enc2utf8() and enc2native() did not always
mark the encoding of the return values when it was known.
dnbinom(x, size = <large>, mu, log = TRUE) no longer
underflows to -Inf for large mu, thanks to a suggestion
from Alessandro Mammana (MPI MolGen, Berlin).
pbeta(x, a, b, log = TRUE) no longer behaves
discontinuously (in a small x-region) because of denormalized
numbers. Also, pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now
terminates “in real time”.
The "CRAN" filter (see available.packages())
no longer removes duplicates other than of packages on CRAN, and
does not fail if there is no CRAN repository in
getOption("repos").
The device listing from dev2bitmap() and
bitmap() was truncated to 1000 characters: modern versions
of GhostScript on most platforms have many more devices.
(Windows.) Commands such as Sys.which() and
pipe() which needed to find the full path to a command
could segfault if the ‘long’ path name was much longer than
the ‘short’ path name (which Sys.which() returns),
as the behaviour of the Windows API call had changed.
R CMD build will fail with an error if one of the
packages specified in the VignetteBuilder field is not
installed. (Without loading those packages it cannot be
ascertained which files are intended to be vignettes. This means
that the VignetteBuilder packages have to be installed for
package checking too.)
(Wish of PR#15775.)
Misguided attempts to use chull() with non-finite
points now give an error (related to PR#15777).
For a formula with exactly 32 variables the 32nd variable was aliased to the intercept in some C-level computations of terms, so that for example attempting to remove it would remove the intercept instead (and leave a corrupt internal structure). (PR#15735)
anyDuplicated() silently returned wrong values when
the first duplicate was at an index which was too large to be
stored in an integer vector (although a lot of RAM and patience
would have been needed to encounter this).
tools::Rd2ex(commentDontrun = FALSE) failed if the
block had only one line.
Hexadecimal constants such as 0x110p-5L which were
incorrectly qualified by L were parsed incorrectly since R
3.0.0, with a slightly garbled warning. (PR#15753)
system() returned success on some platforms even if
the system was unable to launch a process. (PR#15796)
(Windows Rgui console.) Unbuffered output was
sometimes not output immediately if the prompt was not on the last
line of the console.
The built-in help server did not declare the encoding for the ‘DESCRIPTION’ or other text files to be the package encoding, so non-ASCII characters could be displayed incorrectly.
R is now trying harder to not cleanup child processes
that were not spawned by mcparallel() on platforms that
provide information about the source process of the SIGCHLD
signal. This allows 3rd party libraries to manage the exit status
of children that they spawn without R interfering.
mcmapply() was only parallelizing if the number of
jobs was bigger than the number of cores. It now parallelizes if
the number of jobs is more than one.
Auto-printing would re-evaluate its argument when trying to dispatch to a print method. This is now avoided when possible.
Unserializing (including load() and readRDS())
could silently return incorrect numeric values from ASCII saves if
there was a read error.
getParseData() could return incorrect values for
the parents of some elements. (Reported by Andrew Redd.)
Attempting to use data frames of 2^31 or more rows with
merge() or to create a merged data frame of that size now
gives a clearer error message.
parse() did not check its file argument was a
connection if it was not a character string, so
e.g. parse(FALSE) attempted to read from stdin.
Nor did dump() and dput().
The "help.try.all.packages" option was ignored when
the shortcut syntax for help was used, e.g. ?foo.
A potential segfault in string allocation has been fixed. (Found by Radford Neal.)
Potential memory protection errors in sort() and
D() have been fixed. (Found by Radford Neal.)
Fixed a lack of error checking in graphics event functions. (Found by Radford Neal; a different patch used here than the one in pqR.)
numericDeriv() sometimes miscalculated the gradient.
(PR#15849, reported originally by Radford Neal)
CHANGES IN R 3.1.0type.convert() (and hence by default
read.table()) returns a character vector or factor when
representing a numeric input as a double would lose accuracy.
Similarly for complex inputs.
If a file contains numeric data with unrepresentable numbers of
decimal places that are intended to be read as numeric, specify
colClasses in read.table() to be "numeric".
tools::Rdiff(useDiff = FALSE) is closer to the POSIX
definition of diff -b (as distinct from the description
in the man pages of most systems).
New function anyNA(), a version of
any(is.na(.)) which is fast for atomic vectors, based on a
proposal by Tim Hesterberg. (Wish of PR#15239.)
arrayInd(*, useNames = TRUE) and, analogously,
which(*, arr.ind = TRUE) now make use of
names(.dimnames) when available.
is.unsorted() now also works for raw vectors.
The "table" method for as.data.frame() (also
useful as as.data.frame.table()) now passes sep and
base arguments to provideDimnames().
uniroot() gets new optional arguments, notably
extendInt, allowing to auto-extend the search interval when
needed. The return value has an extra component, init.it.
switch(f, ...) now warns when f is a factor,
as this typically happens accidentally where the useR meant to
pass a character string, but f is treated as integer (as
always documented).
The parser has been modified to use less memory.
The way the unary operators (+ - !) handle attributes
is now more consistent. If there is no coercion, all attributes
(including class) are copied from the input to the result:
otherwise only names, dims and dimnames are.
colorRamp() and colorRampPalette() now allow
non-opaque colours and a ramp in opacity via the new argument
alpha = TRUE. (Suggested by Alberto Krone-Martins, but
optionally as there are existing uses which expect only RGB values.)
grid.show.layout() and grid.show.viewport()
get an optional vp.ex argument.
There is a new function find_gs_cmd() in the
tools package to locate a GhostScript executable. (This is
an enhanced version of a previously internal function there.)
object.size() gains a format() method.
There is a new family, "ArialMT", for the
pdf() and postscript() devices. This will only be
rendered correctly on viewers which have access to Monotype
TrueType fonts (which are sometimes requested by journals).
The text and PDF news files, including ‘NEWS’ and ‘NEWS.2’, have been moved to the ‘doc’ directory.
combn(x, simplify = TRUE) now gives a factor result
for factor input x (previously user error).
(Related to PR#15442.)
Added utils::fileSnapshot() and
utils::changedFiles() functions to allow snapshots and
comparison of directories of files.
make.names(names, unique=TRUE) now tries to preserve
existing names. (Suggestion of PR#15452.)
New functions cospi(x), sinpi(x), and
tanpi(x), for more accurate computation of
cos(pi*x), etc, both in R and the C API. Using these
gains accuracy in some cases, e.g., inside lgamma() or
besselI(). (Suggested by Morten Welinder in PR#15529.)
print.table(x, zero.print = ".") now also has an
effect when x is not integer-valued.
There is more support to explore the system's idea of
time-zone names. Sys.timezone() tries to give the current
system setting by name (and succeeds at least on Linux, OS X,
Solaris and Windows), and OlsonNames() lists the names in
the system's Olson database. Sys.timezone(location = FALSE)
gives the previous behaviour.
Platforms with a 64-bit time_t type are allowed to
handle conversions between the "POSIXct" and
"POSIXlt" classes for date-times outside the 32-bit range
(before 1902 or after 2037): the existing workarounds are used on
other platforms. (Note that time-zone information for post-2037
is speculative at best, and the OS services are tested for known
errors and so not used on OS X.)
Currently time_t is usually long and hence 64-bit on
Unix-alike 64-bit platforms: however in several cases the
time-zone database is 32-bit. For R for Windows it is 64-bit
(for both architectures as from this version).
The "save.defaults" option can include a value for
compression_level. (Wish of PR#15579.)
colSums() and friends now have support for arrays and
data-frame columns with 2^31 or more elements.
as.factor() is faster when f is an unclassed
integer vector (for example, when called from tapply()).
fft() now works with longer inputs, from the 12
million previously supported up to 2 billion. (PR#15593)
Complex svd() now uses LAPACK subroutine
ZGESDD, the complex analogue of the routine used for the
real case.
Sweave now outputs ‘.tex’ files in UTF-8 if the
input encoding is declared to be UTF-8, regardless of the
local encoding. The UTF-8 encoding may now be declared using
a LaTeX comment containing the string %\SweaveUTF8
on a line by itself.
file.copy() gains a copy.date argument.
Printing of date-times will make use of the time-zone
abbreviation in use at the time, if known. For example, for Paris
pre-1940 this could be LMT, PMT, WET or
WEST. To enable this, the "POSIXlt" class has an
optional component "zone" recording the abbreviation for
each element.
For platforms which support it, there is also a component
"gmtoff" recording the offset from GMT where known.
(On Windows, by default on OS X and optionally elsewhere.)
The system C function strftime has been replaced by a more
comprehensive version with closer conformance to the POSIX 2008
standard.
dnorm(x, log = FALSE) is more accurate (but somewhat
slower) for |x| > 5; as suggested in PR#15620.
Some versions of the tiff() device have further
compression options.
read.table(), readLines() and scan()
have a new argument to influence the treatment of embedded nuls.
Avoid duplicating the right hand side values in complex
assignments when possible. This reduces copying of replacement
values in expressions such as Z$a <- a0 and
ans[[i]] <- tmp: some package code has relied on there
being copies.
Also, a number of other changes to reduce copying of objects; all contributed by or based on suggestions by Michael Lawrence.
The fast argument of KalmanLike(),
KalmanRun() and KalmanForecast() has been replaced
by update, which instead of updating mod in place,
optionally returns the updated model in an attribute "mod"
of the return value.
arima() and makeARIMA() get a new optional
argument SSinit, allowing the choice of a different
state space initialization which has been observed
to be more reliable close to non-stationarity: see PR#14682.
warning() has a new argument noBreaks., to
simplify post-processing of output with options(warn = 1).
pushBack() gains an argument encoding, to
support reading of UTF-8 characters using scan(),
read.table() and related functions in a non-UTF-8 locale.
all.equal.list() gets a new argument use.names
which by default labels differing components by names (if they
match) rather than by integer index. Saved R output in packages may
need to be updated.
The methods for all.equal() and
attr.all.equal() now have argument check.attributes
after ... so it cannot be partially nor positionally
matched (as it has been, unintentionally).
A side effect is that some previously undetected errors of passing
empty arguments (no object between commas) to all.equal()
are detected and reported.
There are explicit checks that check.attributes is logical,
tolerance is numeric and scale is NULL or
numeric. This catches some unintended positional matching.
The message for all.equal.numeric() reports a
"scaled difference" only for scale != 1.
all.equal() now has a "POSIXt" method
replacing the "POSIXct" method.
The "Date" and "POSIXt" methods of
seq() allows by = "quarter" for completeness
(by = "3 months" always worked).
file.path() removes any trailing separator on
Windows, where they are invalid (although sometimes accepted).
This is intended to enhance the portability of code written by
those using POSIX file systems (where a trailing / can be
used to confine path matching to directories).
New function agrepl() which like grepl()
returns a logical vector.
fifo() is now supported on Windows. (PR#15600)
sort.list(method = "radix") now allows negative
integers (wish of PR#15644).
Some functionality of print.ts() is now available in
.preformat.ts() for more modularity.
mcparallel() gains an option detach = TRUE
which allows execution of code independently of the current
session. It is based on a new estranged = TRUE argument to
mcfork() which forks child processes such that they become
independent of the parent process.
The pdf() device omits circles and text at extremely
small sizes, since some viewers were failing on such files.
The rightmost break for the "months",
"quarters" and "years" cases of
hist.POSIXlt() has been increased by a day. (Inter alia,
fixes PR#15717.)
The handling of DF[i,] <- a where i is of
length 0 is improved. (Inter alia, fixes PR#15718.)
hclust() gains a new method "ward.D2" which
implements Ward's method correctly. The previous "ward"
method is "ward.D" now, with the old name still working.
Thanks to research and proposals by Pierre Legendre.
The sunspot.month dataset has been amended and
updated from the official source, whereas the sunspots and
sunspot.year datasets will remain immutable. The
documentation and source links have been updated correspondingly.
The summary() method for "lm" fits warns if
the fit is essentially perfect, as most of the summary may be
computed inaccurately (and with platform-dependent values).
Programmers who use summary() in order to extract just
a component which will be reliable (e.g., $cov.unscaled)
should wrap their calls in suppressWarnings().
The included version of LAPACK has been updated to 3.5.0.
There is some support for parallel testing of an
installation, by setting TEST_MC_CORES to an integer
greater than one to indicate the maximum number of cores to be
used in parallel. (It is worth specifying at least 8 cores if
available.) Most of these require a make program (such
as GNU make and dmake) which supports the
$MAKE -j nproc syntax.
Except on Windows: the tests of standard package examples in
make check are done in parallel. This also applies to
running tools::testInstalledPackages().
The more time-consuming regression tests are done in parallel.
The package checks in make check-devel and make
check-recommended are done in parallel.
More of make check will work if recommended packages
are not installed: but recommended packages remain needed for
thorough checking of an R build.
The version of tzcode included in ‘src/extra/tzone’ has been updated. (Formerly used only on Windows.)
The included (64-bit) time-zone conversion code and Olson
time-zone database can be used instead of the system version: use
configure option --with-internal-tzcode. This
is the default on Windows and OS X. (Note that this does not
currently work if a non-default rsharedir
configure variable is used.)
(It might be necessary to set environment variable TZ on OSes where this is not already set, although the system timezone is deduced correctly on at least Linux, OS X and Windows.)
This option also switches to the version of strftime
included in directory ‘src/extra/tzone’.
configure now tests for a C++11-compliant compiler
by testing some basic features. This by default tries flags for
the compiler specified by CXX, but an alternative compiler,
options and standard can be specified by variables CXX1X,
CXX1XFLAGS and CXX1XSTD (e.g., -std=gnu++11).
R can now optionally be compiled to use reference
counting instead of the NAMED mechanism by defining
SWITCH_TO_REFCNT in ‘Rinternals.h’. This may become
the default in the future.
There is a new option --use-system-tre to use a
suitable system tre library: at present this means a version
from their git repository, after corrections.
(Wish of PR#15660.)
The CRANextra repository is no longer a default
repository on Windows: all the binary versions of packages from
CRAN are now on CRAN, although CRANextra contains packages
from Omegahat and elsewhere used by CRAN packages.
Only vignettes sources in directory ‘vignettes’ are considered to be vignettes and hence indexed as such.
In the ‘DESCRIPTION’ file,
License: X11
is no longer recognized as valid. Use MIT or BSD_2_clause instead, both of which need + file LICENSE.
For consistency, entries in ‘.Rinstignore’ are now matched case-insensitively on all platforms.
Help for S4 methods with very long signatures now tries harder to split the description in the Usage field to no more than 80 characters per line (some packages had over 120 characters).
R CMD INSTALL --build (not Windows) now defaults to
the internal tar() unless R_INSTALL_TAR is set.
There is support for compiling C++11 code in packages on suitable platforms: see ‘Writing R Extensions’.
Fake installs now install the contents of directory ‘inst’: some packages use this to install e.g. C++ headers for use by other packages that are independent of the package itself. Option --no-inst can be used to get the previous behaviour.
The behaviour of the code browser has been made more consistent, in part following the suggestions in PR#14985.
Calls to browser() are now consistent with calls
to the browser triggered by debug(), in that Enter
will default to n rather than c.
A new browser command s has been added, to
“step into” function calls.
A new browser command f has been added, to
“finish” the current loop or function.
Within the browser, the command help will
display a short list of available commands.
Only vignettes sources in directory ‘vignettes’ are
considered to be vignettes by R CMD check. That has
been the preferred location since R 2.14.0 and is now obligatory.
For consistency, R CMD build now matches entries
in ‘.Rbuildignore’ and ‘vignettes/.install_extras’
case-insensitively on all platforms (not just on Windows).
checkFF() (called by R CMD check by
default) can optionally check foreign function calls for
consistency with the registered type and argument count. This is
the default for R CMD check --as-cran or can be enabled
by setting environment variable _R_CHECK_FF_CALLS_ to
registration (but is in any case suppressed by
--install=no). Because this checks calls in which
.NAME is an R object and not just a literal character
string, some other problems are detected for such calls.
Functions suppressForeignCheck() and dontCheck()
have been added to allow package authors to suppress false
positive reports.
R CMD check --as-cran warns about a false value of
the ‘DESCRIPTION’ field BuildVignettes for Open Source
packages, and ignores it. (An Open Source package needs to have
complete sources for its vignettes which should be usable on a
suitably well-equipped system).
R CMD check --no-rebuild-vignettes is defunct:
R CMD check --no-build-vignettes has been preferred since
R 3.0.0.
R CMD build --no-vignettes is defunct:
R CMD build --no-build-vignettes has been preferred since
R 3.0.0.
R CMD Sweave and R CMD Stangle now
process both Sweave and non-Sweave vignettes. The
tools::buildVignette() function has been added to do the
same tasks from within R.
The flags returned by R CMD config --ldflags and
(where installed) pkg-config --libs libR are now those
needed to link a front-end against the (shared or static) R
library.
‘Sweave.sty’ has a new option [inconsolata].
R CMD check customizations such as
_R_CHECK_DEPENDS_ONLY_ make available packages only in
LinkingTo only for installation, and not for
loading/runtime tests.
tools::checkFF() reports on .C and
.Fortran calls with DUP = FALSE if argument
check_DUP is true. This is selected by
R CMD check by default.
R CMD check --use-gct can be tuned to
garbage-collect less frequently using gctorture2()
via the setting of environment variable
_R_CHECK_GCT_N_.
Where supported, tools::texi2dvi() limits the number
of passes tried to 20.
(Windows only) A function R_WaitEvent() has been
added (with declaration in header‘R.h’) to block execution
until the next event is received by R.
Remapping in the ‘Rmath.h’ header can be suppressed by defining R_NO_REMAP_RMATH.
The remapping of rround() in header ‘Rmath.h’
has been removed: use fround() instead.
ftrunc() in header ‘Rmath.h’ is now a wrapper
for the C99 function trunc(), which might as well be used
in C code: ftrunc() is still needed for portable C++ code.
The never-documented remapping of prec() to
fprec() in header ‘Rmath.h’ has been removed.
The included LAPACK subset now contains ZGESDD and
ZGELSD.
The function LENGTH() now checks that it is only
applied to vector arguments. However, in packages length()
should be used. (In R itself LENGTH() is a macro without
the function overhead of length().)
Calls to SET_VECTOR_ELT() and SET_STRING_ELT()
are now checked for indices which are in-range: several packages
were writing one element beyond the allocated length.
allocVector3 has been added which allows custom
allocators to be used for individual vector allocations.
chol(pivot = TRUE, LINPACK = TRUE) is defunct.
Arguments EISPACK for eigen() and LINPACK for
chol(), chol2inv(), solve() and svd()
are ignored: LAPACK is always used.
.find.package() and .path.package() are
defunct: only the versions without the initial dot introduced in
R 2.13.0 have ever been in the API.
Partial matching when using the $ operator on
data frames now throws a warning and may become defunct in the
future. If partial matching is intended, replace foo$bar
by foo[["bar", exact = FALSE]].
The long-deprecated use of \synopsis in the
Usage section of ‘.Rd’ files has been removed: such
sections are now ignored (with a warning).
package.skeleton()'s deprecated argument
namespace has been removed.
Many methods are no longer exported by package stats. They are all registered on their generic, which should be called rather than calling a method directly.
Functions readNEWS() and checkNEWS() in
package tools are defunct.
download.file(method = "lynx") is deprecated.
.C(DUP = FALSE) and .Fortran(DUP = FALSE) are
now deprecated, and may be disabled in future versions of R. As
their help has long said, .Call() is much preferred.
R CMD check notes such usages (by default).
The workaround of setting R_OSX_VALGRIND has been removed: it is not needed in current valgrind.
Calling lm.wfit() with no non-zero weights gave an
array-overrun in the Fortran code and a not very sensible answer.
It is now special-cased with a simpler answer (no qr
component).
Error messages involving non-syntactic names (e.g., as produced
by `\r` when that object does not exist) now encode
the control characters. (Reported by Hadley Wickham.)
getGraphicsEvent() caused 100% usage of one CPU in
Windows. (PR#15500)
nls() with no start argument may now work
inside another function (scoping issue).
pbeta() and similar work better for very large
(billions) ncp.
Where time zones have changed abbreviations over the years,
the software tries to more consistently use the abbreviation
appropriate to the time or if that is unknown, the current
abbreviation. On some platforms where the C function
localtime changed the tzname variables the reported
abbreviation could have been that of the last time converted.
all.equal(list(1), identity) now works.
Bug fix for pushing viewports in grid (reported by JJ Allaire and Kevin Ushey).
NOTE for anyone poking around within the graphics engine display list (despite the warnings not to) that this changes what is recorded by grid on the graphics engine display list.
Extra checks have been added for unit resolution and conversion in grid, to catch instances of division-by-zero. This may introduce error messages in existing code and/or produce a different result in existing code (but only where a non-finite location or dimension may now become zero).
Some bugs in TRE have been corrected by updating from the
git repository. This allows R to be installed on some
platforms for which this was a blocker (PR#15087 suggests Linux
on ARM and HP-UX).
? applied to a call to an S4 generic failed in
several cases. (PR#15680)
The implicit S4 generics for primitives with ... in
their argument list were incorrect. (PR#15690)
Bug fixes to methods::callGeneric(). (PR#15691)
The bug fix to aggregrate() in PR#15004 introduced
a new bug in the case of no grouping variables. (PR#15699)
In rare cases printing deeply nested lists overran a buffer by one byte and on a few platforms segfaulted. (PR#15679)
The dendrogram method of as.dendrogram() was hidden
accidentally, (PR#15703), and order.dendrogram(d) gave
too much for a leaf d. (PR#15702)
R would try to kill processes on exit that have pids ever
used by a child process spawned by mcparallel even though
the current process with that pid was not actually its child.
cophenetic() applied to a "dendrogram" object
sometimes incorrectly returned a "Labels" attribute with
dimensions. (PR#15706)
printCoefmat() called from quite a few print()
methods now obeys small getOption("width") settings,
line wrapping the "signif. codes" legend appropriately.
(PR#15708)
model.matrix() assumed that the stored dimnames for a
matrix was NULL or length 2, but length 1 occurred.
The clipping region for a device was sometimes used in base graphics before it was set.
CHANGES IN R 3.0.3 On Windows there is support for making ‘.texi’ manuals
using texinfo 5.0 or later: the setting is in file
‘src/gnuwin32/MkRules.dist’.
A packaging of the Perl script and modules for texinfo
5.2 has been made available at
http://www.stats.ox.ac.uk/pub/Rtools/.
write.table() now handles matrices of
2^31 or more elements, for those with large amounts
of patience and disc space.
There is a new function, La_version(), to report the
version of LAPACK in use.
The HTML version of ‘An Introduction to R’ now has links to PNG versions of the figures.
There is some support to produce manuals in ebook formats. (See ‘doc/manual/Makefile’. Suggested by Mauro Cavalcanti.)
On a Unix-alike Sys.timezone() returns NA if
the environment variable TZ is unset, to distinguish it from
an empty string which on some OSes means the UTC time zone.
The backtick may now be escaped in strings, to allow names
containing them to be constructed, e.g. `\``. (PR#15621)
read.table(), readLines() and scan()
now warn when an embedded nul is found in the input. (Related to
PR#15625 which was puzzled by the behaviour in this unsupported
case.)
(Windows only.) file.symlink() works around the
undocumented restriction of the Windows system call to
backslashes. (Wish of PR#15631.)
KalmanForecast(fast = FALSE) is now the default, and
the help contains an example of how fast = TRUE can be used
in this version. (The usage will change in 3.1.0.)
strptime() now checks the locale only when
locale-specific formats are used and caches the locale in use:
this can halve the time taken on OSes with slow system
functions (e.g., OS X).
strptime() and the format() methods for
classes "POSIXct", "POSIXlt" and "Date"
recognize strings with marked encodings: this allows, for example,
UTF-8 French month names to be read on (French) Windows.
iconv(to = "utf8") is now accepted on all platforms
(some implementations did already, but GNU libiconv did not:
however converted strings were not marked as being in UTF-8). The
official name, "UTF-8" is still preferred.
available.packages() is better protected against
corrupt metadata files. (A recurring problem with Debian package
shogun-r: PR#14713.)
Finalizers are marked to be run at garbage collection, but
run only at a somewhat safer later time (when interrupts are
checked). This circumvents some problems with finalizers running
arbitrary code during garbage collection (the known instances being
running options() and (C-level) path.expand()
re-entrantly).
The included version of PCRE has been updated to 8.34. This fixes bugs and makes the behaviour closer to Perl 5.18. In particular, the concept of ‘space’ includes VT and hence agrees with POSIX's.
The new field SysDataCompression in the ‘DESCRIPTION’ file allows user control over the compression used for ‘sysdata.rda’ objects in the lazy-load database.
install.packages(dependencies = value) for value =
NA (the default) or value = TRUE omits packages only in
LinkingTo for binary package installs.
The long undocumented remapping of rround() to
Rf_fround() in header ‘Rmath.h’ is now formally
deprecated: use fround() directly.
Remapping of prec() and trunc() in the
‘Rmath.h’ header has been disabled in C++ code (it has caused
breakage with libc++ headers).
getParseData() truncated the imaginary part of
complex number constants. (Reported by Yihui Xie.)
dbeta(x, a, b) with a or b within a
factor of 2 of the largest representable number could
infinite-loop. (Reported by Ioannis Kosmidis.)
provideDimnames() failed for arrays with a 0
dimension. (PR#15465)
rbind() and cbind() did not handle
list objects correctly. (PR#15468)
replayPlot() now checks if it is replaying a plot
from the same session.
rasterImage() and grid.raster() now give
error on an empty (zero-length) raster. (Reported by Ben North.)
plot.lm() would sometimes scramble the labels
in plot type 5. (PR#15458 and PR#14837)
min() did not handle NA_character_ values
properly. (Reported by Magnus Thor Torfason.)
(Windows only.) readRegistry() would duplicate
default values for keys. (PR#15455)
str(..., strict.width = "cut") did not handle
it properly when more than one line needed to be cut. (Reported
by Gerrit Eichner.)
Removing subclass back-references when S4 classes were removed or their namespace unloaded had several bugs (e.g., PR#15481).
aggregate() could fail when there were too many
levels present in the by argument. (PR#15004)
namespaceImportFrom() needed to detect primitive
functions when checking for duplicated imports (reported by
Karl Forner).
getGraphicsEvent() did not exit when a user closed
the graphics window. (PR#15208)
Errors in vignettes were not always captured and displayed properly. (PR#15495)
contour() could fail when dealing with extremely
small z values. (PR#15454)
Several functions did not handle zero-length vectors properly,
including browseEnv(), format(), gl(),
relist() and summary.data.frame(). (E.g., PR#15499)
Sweave() did not restore the R output to the
console if it was interrupted by a user in the middle of evaluating
a code chunk. (Reported by Michael Sumner.)
Fake installs of packages with vignettes work again.
Illegal characters in the input caused parse()
(and thus source()) to segfault. (PR#15518)
The nonsensical use of nmax = 1 in
duplicated() or unique() is now silently ignored.
qcauchy(p, *) is now fully accurate even when p is
very close to 1. (PR#15521)
The validmu() and valideta() functions in the
standard glm() families now also report non-finite values,
rather than failing.
Saved vignette results (in a ‘.Rout.save’ file) were
not being compared to the new ones during R CMD check.
Double-clicking outside of the list box (e.g., on the scrollbar)
of a Tk listbox widget generated by tk_select.list() no
longer causes the window to close. (PR#15407)
Improved handling of edge cases in
parallel::splitindices(). (PR#15552)
HTML display of results from help.search() and
?? sometimes contained badly constructed links.
c() and related functions such as unlist()
converted raw vectors to invalid logical vectors. (PR#15535)
(Windows only) When a call to system2() specified
one of stdin, stdout or stderr to be a file,
but the command was not found (e.g., it contained its arguments,
or the program was not on the PATH), it left the file open
and unusable until R terminated. (Reported by Mathew McLean.)
The bmp() device was not recording res = NA
correctly: it is now recorded as 72 ppi.
Several potential problems with compiler-specific behaviour
have been identified using the ‘Undefined Behaviour
Sanitizer’ in conjunction with the clang compiler.
hcl() now honours NA inputs (previously they
were mapped to black).
Some translations in base packages were being looked up in the main catalog rather than that for the package.
As a result of the 3.0.2 change about ‘the last
second before the epoch’, most conversions which should have given
NA returned that time. (The platforms affected include
Linux and OS X, but not Windows nor Solaris.)
rowsum() has more support for matrices and dataframes
with 2^31 or more elements. (PR#15587)
predict(<lm object>, interval = "confidence", scale =
<something>) now works. (PR#15564)
The bug fix in 3.0.2 for PR#15411 was too aggressive, and sometimes removed spaces that should not have been removed. (PR#15583)
Running R code in a tcltk callback failed to set the busy flag, which will be needed to tell OS X not to ‘App Nap’.
The code for date-times before 1902 assumed that the offset from GMT in 1902 was a whole number of minutes: that was not true of Paris (as recorded on some platforms).
Using Sys.setlocale to set LC_NUMERIC to
"C" (to restore the sane behavior) no longer gives a
warning.
deparse() now deparses complex vectors in a way that
re-parses to the original values. (PR#15534, patch based on code
submitted by Alex Bertram.)
In some extreme cases (more than 10^15)
integer inputs to dpqrxxx() functions might have been
rounded up by one (with a warning about being non-integer).
(PR#15624)
Plotting symbol pch = 14 had the triangle upside down
on some devices (typically screen devices). The triangle is
supposed to be point up. (Reported by Bill Venables.)
getSrcref() did not work on method definitions if
rematchDefinition() had been used.
KalmanForecast(fast = FALSE) reported a (harmless)
stack imbalance.
The count of observations used by KalmanRun() did not
take missing values into account.
In locales where the abbreviated name of one month is a
partial match for the full name of a later one, the %B
format in strptime() could fail. An example was French on
OS X, where juin is abbreviated to jui and partially
matches juillet. Similarly for weekday names.
pbeta(x, a, b, log.p = TRUE) sometimes underflowed to
zero for very small and very differently sized a, b.
(PR#15641)
approx() and approxfun() now handle infinite
values with the "constant" method. (PR#15655)
stripchart() again respects reversed limits in
xlim and ylim. (PR#15664)
CHANGES IN R 3.0.2The ‘NEWS’ files have been re-organized.
This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y and 2.x.y releases is in files ‘NEWS.0’, ‘NEWS.1’ and ‘NEWS.2’. The latter files are now installed when R is installed. An HTML version of news from 2.10.0 to 2.15.3 is available as ‘doc/html/NEWS.2.html’.
sum() for integer arguments now uses an integer
accumulator of at least 64 bits and so will be more accurate in
the very rare case that a cumulative sum exceeds
2^53 (necessarily summing more than 4 million
elements).
The example() and tools::Rd2ex() functions now
have parameters to allow them to ignore \dontrun markup in
examples. (Suggested by Peter Solymos.)
str(x) is considerably faster for very large lists,
or factors with 100,000 levels, the latter as in PR#15337.
col2rgb() now converts factors to character strings
not integer codes (suggested by Bryan Hanson).
tail(warnings()) now works, via the new `[`
method.
There is now support for the LaTeX style file ‘zi4.sty’ which has in some distributions replaced ‘inconsolata.sty’.
unlist(x) now typically returns all non-list
xs unchanged, not just the “vector” ones.
Consequently, format(lst) now also works when the list
lst has non-vector elements.
The tools::getVignetteInfo() function has been added
to give information about installed vignettes.
New assertCondition(), etc. utilities in tools, useful
for testing.
Profiling now records non-inlined calls from byte-compiled
code to BUILTIN functions.
Various functions in stats and elsewhere that use
non-standard evaluation are now more careful to follow the
namespace scoping rules. E.g., stats::lm() can now find
stats::model.frame() even if stats is not on the
search path or if some package defines a function of that name.
If an invalid/corrupt .Random.seed object is
encountered in the workspace it is ignored with a warning rather
than giving an error. (This allows R itself to rely on a working
RNG, e.g. to choose a random port.)
seq() and seq.int() give more explicit error
messages if called with invalid (e.g., NaN) inputs.
When parse() finds a syntax error, it now makes
partial parse information available up to the location of the
error. (Request of Reijo Sund.)
Methods invoked by NextMethod() had a different
dynamic parent to the generic. This was causing trouble where S3
methods invoked via lazy evaluation could lose track of their
generic. (PR#15267)
Code for the negative binomial distribution now treats the case
size == 0 as a one-point distribution at zero.
abbreviate() handles without warning non-ASCII input
strings which require no abbreviation.
read.dcf() no longer has a limit of 8191 bytes per
line. (Wish of PR#15250.)
formatC(x) no longer copies the class of x to
the result, to avoid misuse creating invalid objects as in
PR#15303. A warning is given if a class is discarded.
Dataset npk has been copied from MASS to
allow more tests to be run without recommended packages being
installed.
The initialization of the regression coefficients for
non-degenerate differenced models in arima() has been
changed and in some examples avoids a local maximum. (PR#15396)
termplot() now has an argument transform.x
to control the display of individual terms in the plot.
(PR#15329)
format() now supports digits = 0, to
display nsmall decimal places.
There is a new read-only par() parameter called
"page", which returns a logical value indicating whether
the next plot.new() call will start a new page.
Processing Sweave and Rd documents to PDF now renders backticks and single quotes better in several instances, including in \code and \samp expressions.
utils::modifyList() gets a new argument keep.null
allowing NULL components in the replacement to be retained,
instead of causing corresponding components to be deleted.
tools::pkgVignettes() gains argument check;
if set to TRUE, it will warn when it appears a vignette requests
a non-existent vignette engine.
R CMD check --as-cran checks the line widths in
usage and examples sections of the package Rd files.
R CMD check --as-cran now implies --timings.
R CMD check looks for command gfile if a
suitable file is not found. (Although file is
not from GNU, OpenCSW on Solaris installs it as gfile.)
R CMD build (with the internal tar) checks
the permissions of ‘configure’ and ‘cleanup’ files and
adds execute permission to the recorded permissions for these
files if needed, with a warning. This is useful on OSes and file
systems which do not support execute permissions (notably, on
Windows).
R CMD build now weaves and tangles all vignettes,
so suggested packages are not required during package installation
if the source tarball was prepared with current
R CMD build.
checkFF() (used by R CMD check) does a
better job of detecting calls from other packages, including not
reporting those where a function has been copied from another
namespace (e.g., as a default method). It now reports calls where
.NAME is a symbol registered in another package.
On Unix-alike systems, R CMD INSTALL now installs packages
group writably whenever the library (lib.loc) is group
writable. Hence, update.packages() works for other group
members (suggested originally and from a patch by Dirk Eddelbuettel).
R CMD javareconf now supports the use of symbolic
links for JAVA_HOME on platforms which have
realpath. So it is now possible to
use
R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-1.7.0
on a Linux system and record that value rather than the frequently-changing full path such as ‘/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64’.
(Windows only.) Rscript -e requires a non-empty
argument for consistency with Unix versions of R. (Also
Rterm -e and R -e.)
R CMD check does more thorough checking of
declared packages and namespaces. It reports
packages declared in more than one of the Depends, Imports, Suggests and Enhances fields of the ‘DESCRIPTION’ file.
namespaces declared in Imports but not
imported from, neither in the ‘NAMESPACE’ file nor using
the :: nor ::: operators.
packages which are used in library() or
requires() calls in the R code but were already put on
the search path via Depends.
packages declared in Depends not imported via the ‘NAMESPACE’ file (except the standard packages). Objects used from Depends packages should be imported to avoid conflicts and to allow correct operation when the namespace is loaded but not attached.
objects imported via ::: calls where
:: would do.
objects imported by :: which are not exported.
objects imported by ::: calls which do not exist.
See ‘Writing R Extensions’ for good practice.
R CMD check optionally checks for non-standard
top-level files and directories (which are often mistakes): this
is enabled for --as-cran.
LaTeX style file upquote.sty is no longer included
(the version was several years old): it is no longer used in R.
A much later version is commonly included in LaTeX distributions
but does not play well with the ae fonts which are the
default for Sweave vignettes.
R CMD build makes more use of the ‘build’
sub-directory of package sources, for example to record
information about the vignettes.
R CMD check analyses ::: calls.
The macros used for the texinfo manuals have been changed to
work better with the incompatible changes made in texinfo
5.x.
The minimum version for a system xz library is now
5.0.3 (was 4.999). This is in part to avoid 5.0.2, which can
compress in ways other versions cannot decompress.
The included version of PCRE has been updated to 8.33.
The included version of zlib has been updated to
1.2.8, a bug-fix release.
The included version of xz utils's liblzma has been
updated to 5.0.5.
Since javareconf (see above) is used when R is
installed, a stable link for JAVA_HOME can be supplied then.
Configuring with --disable-byte-compilation will override the ‘DESCRIPTION’ files of recommended packages, which typically require byte-compilation.
More of the installation and checking process will work even
when TMPDIR is set to a path containing spaces, but this is
not recommended and external software (such as
texi2dvi) may fail.
Installation is aborted immediately if a LinkingTo
package is not installed.
R CMD INSTALL has a new option
--no-byte-compile which will override a ByteCompile
field in the package's ‘DESCRIPTION’ file.
License BSD is deprecated: use BSD_3_clause or BSD_2_clause instead.
License X11 is deprecated: use MIT or BSD_2_clause instead.
Version requirements for LinkingTo packages are now
recognized: they are checked at installation. (Fields with
version requirements were previously silently ignored.)
The limit of 500 S3method entries in a
NAMESPACE file has been removed.
The default ‘version’ of Bioconductor for its packages has been changed to the upcoming 2.13, but this can be set by the environment variable R_BIOC_VERSION when R is installed.
‘Rdefines.h’ has been tweaked so it can be included in C++ code after ‘R_ext/Boolean.h’ (which is included by ‘R.h’).
Note that ‘Rdefines.h’ is not kept up-to-date, and ‘Rinternals.h’ is preferred for new code.
eval and applyClosure are now protected
against package code supplying an invalid rho.
The unused namespace argument to
package.skeleton() is now formally deprecated and will be
removed in R 3.1.0.
plclust() is deprecated: use the plot() method
for class "hclust" instead.
Functions readNEWS() and checkNEWS() in
package tools are deprecated (and they have not worked with
current ‘NEWS’ files for a long time).
‘An Introduction to R’ has a new chapter on using R as a scripting language including interacting with the OS.
help.request() could not determine the current version
of R on CRAN. (PR#15241)
On Windows, file.info() failed on root directories unless
the path was terminated with an explicit ".". (PR#15302)
The regmatches<-() replacement function mishandled
results coming from regexpr(). (PR#15311)
The help for setClass() and
representation() still suggested the deprecated argument
representation=. (PR#15312)
R CMD config failed in an installed build of R
3.0.1 (only) when a sub-architecture was used. (Reported by
Berwin Turlach.)
On Windows, the installer modified the ‘etc/Rconsole’ and ‘etc/Rprofile.site’ files even when default options were chosen, so the MD5 sums did not refer to the installed versions. (Reported by Tal Galili.)
plot(hclust(), cex =) respects cex again
(and possibly others similarly). (Reported by Peter Langfelder.)
If multiple packages were checked by R CMD check,
and one was written for a different OS, it would set
--no-install for all following packages as well as
itself.
qr.coef() and related functions did not properly coerce
real vectors to complex when necessary. (PR#15332)
ftable(a) now fixes up empty dimnames such
that the result is printable.
package.skeleton() was not starting its search for
function objects in the correct place if environment was
supplied. (Reported by Karl Forner.)
Parsing code was changing the length field of vectors and confusing the memory manager. (PR#15345)
The Fortran routine ZHER2K in the reference BLAS
had a comment-out bug in two places.
This caused trouble with eigen() for Hermitian matrices.
(PR#15345 and report from Robin Hankin)
vignette() and browseVignettes() did not
display non-Sweave vignettes properly.
Two warning/error messages have been corrected:
the (optional) warning produced by a partial name match
with a pairlist, the error message from a zero-length argument to
the : operator. (Found by Radford Neal; PR#15358,
PR#15356)
svd() returned NULL rather than omitting
components as documented. (Found by Radford Neal; PR#15360)
mclapply() and mcparallel() with
silent = TRUE could break a process that uses
stdout output
unguarded against broken pipes (e.g., zip will fail
silently). To work around such issues, they now replace
stdout with a descriptor pointed to ‘/dev/null’
instead. For this purpose, internal closeStdout and
closeStderr functions have gained the to.null flag.
log(), signif() and round() now raise an
error if a single named argument is not named x. (PR#15361)
deparse() now deparses raw vectors in a form that
is syntactically correct. (PR#15369)
The jpeg driver in Sweave created a JPEG file, but gave
it a ‘.png’ extension. (PR#15370)
Deparsing of infix operators with named arguments is improved. (PR#15350)
mget(), seq.int() and numericDeriv()
did not duplicate arguments properly. (PR#15352, PR#15353,
PR#15354)
kmeans(algorithm = "Hartigan-Wong") now always stops
iterating in the QTran stage. (PR#15364).
read.dcf() re-allocated incorrectly and so could
segfault when called on a file with lines of more than 100 bytes.
On systems where mktime() does not set errno,
the last second before the epoch could not be converted from
POSIXlt to POSIXct. (Reported by Bill Dunlap.)
add1.glm() miscalculated F-statistics when df > 1. (Bill
Dunlap, PR#15386).
stem() now discards infinite inputs rather than
hanging. (PR#15376)
The parser now enforces C99 syntax for floating point
hexadecimal constants (e.g., 0x1.1p0), rather than returning
unintended values for malformed constants. (PR#15234)
model.matrix() now works with very long LHS
names (more than 500 bytes). (PR#15377)
integrate() reverts to the pre-2.12.0 behaviour: from
2.12.0 to 3.0.1 it sometimes failed to achieve the requested
tolerance and reported error estimates that were exceeded.
(PR#15219)
strptime() now handles %W fields with value
0. (PR#15915)
R is now better protected against people trying to interact with the console in startup code. (PR#15325)
Subsetting 1D arrays often lost dimnames (PR#15301).
Unary + on a logical vector did not coerce to
integer, although unary - did.
na.omit() and na.exclude() added a row
to a zero-row data frame. (PR#15399)
All the (where necessary cut-down) vignettes are installed if R was configured with --without-recommended-packages.
source() did not display filenames when reporting
syntax errors.
Syntax error reports misplaced the caret pointing out the bad token.
(Windows only) Starting R with R (instead of
Rterm or Rgui) would lose any
zero-length strings from the command line arguments. (PR#15406)
Errors in the encoding specified on the command line via
--encoding=foo were not handled properly. (PR#15405)
If x is a symbol, is.vector(x, "name") now
returns TRUE, since "name" and "symbol"
should be synonyms. (Reported by Hervé Pagès.)
R CMD rtags works on platforms (such as OS X)
with a XSI-conformant shell command echo. (PR#15231)
is.unsorted(NA) returns false as documented (rather than
NA).
R CMD LINK did not know about sub-architectures.
system() and system2() are better protected
against users who misguidedly have spaces in the temporary
directory path.
file.show() and edit() are now more likely to
work on file paths containing spaces. (Where external utilities
are used, not the norm on Windows nor in R.app which
should previously have worked.)
Packages using the methods package are more likely to work when they import it but it is not attached. (Several parts of its C code were looking for its R functions on the search path rather than in its namespace.)
lgamma(-x) is no longer NaN for very small x.
(Windows) system2() now respects specifying
stdout and stderr as files if called from
Rgui. (PR#15393)
Closing an x11() device whilst locator() or
identify() is in progress no longer hangs R. (PR#15253)
list.dirs(full.names = FALSE) was not implemented.
(PR#15170)
format() sometimes added unnecessary spaces.
(PR#15411)
all.equal(check.names = FALSE) would ignore the request
to ignore the names and would check them as attributes.
The symbol set by tools::Rd2txt_options(itemBullet=)
was not respected in some locales. (PR#15435)
mcMap() was not exported by package
parallel. (PR#15439)
plot() for TukeyHSD objects did not balance
dev.hold() and dev.flush() calls on multi-page plots.
(PR#15449)
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.preschedule = 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 time zone 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 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: yes
to 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: X11
is 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".
Older news can be found in text format in files NEWS.0, NEWS.1 and NEWS.2 in the ‘doc’ directory. News in HTML format for R versions from 2.10.0 to 2.15.3 is in NEWS.2.html.