attach() reports conflicts, it does so
library() by using
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 = FALSE no longer remove any created files.
buildvignette() gains a
keep argument for more
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.
read.table() and similar
read.*() functions get a new
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
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
rbeta() are now defined also for a = 0, b = 0,
or infinite a and b (where they typically returned
Many package authors report that the RStudio graphics device
does not work correctly with their package's use of
dev.new(). The new option
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
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
Package help requests like
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
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
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’
Compilers/linkers were handling the visibility controls 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’.
are slightly less restrictive in checking if
integer-valued. (Wish of PR#15734.)
pchisq(x, df, ncp, log.p = TRUE) is more accurate and
no longer underflows for small
ncp < 80, e.g,
pchisq(1e-5, df = 100, ncp = 1, log = TRUE).
(Based on PR#15635 and a suggestion by Roby Joehanes.)
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
+1400 can occur). (PR#15768)
png(type = "cairo", antialias = "gray")
was not accepted. (PR#15760)
save(..., envir=) with named objects could
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)
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
pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now
terminates “in real time”.
"CRAN" filter (see
no longer removes duplicates other than of packages on CRAN, and
does not fail if there is no CRAN repository in
The device listing from
bitmap() was truncated to 1000 characters: modern versions
of GhostScript on most platforms have many more devices.
(Windows.) Commands such as
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
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)
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
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.
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
parse(FALSE) attempted to read from
"help.try.all.packages" option was ignored when
the shortcut syntax for help was used, e.g.
A potential segfault in string allocation has been fixed. (Found by Radford Neal.)
Potential memory protection errors in
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)
type.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
read.table() to be
tools::Rdiff(useDiff = FALSE) is closer to the POSIX
diff -b (as distinct from the description
man pages of most systems).
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
"table" method for
as.data.frame.table()) now passes
base arguments to
uniroot() gets new optional arguments, notably
extendInt, allowing to auto-extend the search interval when
needed. The return value has an extra component,
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
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.
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.)
get an optional
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
There is a new family,
"ArialMT", for the
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.)
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.)
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
besselI(). (Suggested by Morten Welinder in PR#15529.)
print.table(x, zero.print = ".") now also has an
x is not integer-valued.
There is more support to explore the system's idea of
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
"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.)
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).
"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
fft() now works with longer inputs, from the 12
million previously supported up to 2 billion. (PR#15593)
svd() now uses LAPACK subroutine
ZGESDD, the complex analogue of the routine used for the
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
on a line by itself.
file.copy() gains a
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
"zone" recording the abbreviation for
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
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
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
Also, a number of other changes to reduce copying of objects; all contributed by or based on suggestions by Michael Lawrence.
fast argument of
KalmanForecast() has been replaced
update, which instead of updating
mod in place,
optionally returns the updated model in an attribute
of the return value.
makeARIMA() get a new optional
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
simplify post-processing of output with
options(warn = 1).
pushBack() gains an argument
support reading of UTF-8 characters using
read.table() and related functions in a non-UTF-8 locale.
all.equal.list() gets a new argument
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
attr.all.equal() now have argument
... 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
are detected and reported.
There are explicit checks that
check.attributes is logical,
tolerance is numeric and
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" methods of
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).
agrepl() which like
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.
pdf() device omits circles and text at extremely
small sizes, since some viewers were failing on such files.
The rightmost break for the
"years" cases of
hist.POSIXlt() has been increased by a day. (Inter alia,
The handling of
DF[i,] <- a where
i is of
length 0 is improved. (Inter alia, fixes PR#15718.)
hclust() gains a new method
implements Ward's method correctly. The previous
"ward.D" now, with the old name still working.
Thanks to research and proposals by Pierre Legendre.
sunspot.month dataset has been amended and
updated from the official source, whereas the
sunspot.year datasets will remain immutable. The
documentation and source links have been updated correspondingly.
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.
should wrap their calls in
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
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
The more time-consuming regression tests are done in parallel.
The package checks in
make check-devel and
check-recommended are done in parallel.
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
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
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
git repository, after corrections.
(Wish of PR#15660.)
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: X11is 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
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.
browser() are now consistent with calls
to the browser triggered by
debug(), in that Enter
will default to
n rather than
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
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.
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.
have been added to allow package authors to suppress false
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 CMD build --no-vignettes is defunct:
R CMD build --no-build-vignettes has been preferred since
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
pkg-config --libs libR are now those
needed to link a front-end against the (shared or static) R
‘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
tools::checkFF() reports on
.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
via the setting of environment variable
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
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
fprec() in header ‘Rmath.h’ has been removed.
The included LAPACK subset now contains
LENGTH() now checks that it is only
applied to vector arguments. However, in packages
should be used. (In R itself
LENGTH() is a macro without
the function overhead of
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.
are ignored: LAPACK is always used.
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", 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.
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.
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
Error messages involving non-syntactic names (e.g. as produced
`\r` when that object does not exist) now encode
the control characters. (Reported by Hadley Wickham.)
getGraphicsEvent() caused 100% usage of one CPU in
nls() with no
start argument may now work
inside another function (scoping issue).
pbeta() and similar work better for very large
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
their argument list were incorrect. (PR#15690)
Bug fixes to
In rare cases printing deeply nested lists overran a buffer by one byte and on a few platforms segfaulted. (PR#15679)
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
sometimes incorrectly returned a
"Labels" attribute with
printCoefmat() called from quite a few
methods now obeys small
line wrapping the "signif. codes" legend appropriately.
model.matrix() assumed that the stored dimnames for a
NULL or length 2, but length 1 occurred.
The clipping region for a device was sometimes used in base graphics before it was set.
On Windows there is support for making ‘.texi’ manuals
texinfo 5.0 or later: the setting is in file
A packaging of the Perl script and modules for
5.2 has been made available at
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
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.
now warn when an embedded nul is found in the input. (Related to
PR#15625 which was puzzled by the behaviour in this unsupported
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
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
"UTF-8" is still preferred.
available.packages() is better protected against
corrupt metadata files. (A recurring problem with Debian package
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
options() and (C-level)
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
NA (the default) or
value = TRUE omits packages only in
LinkingTo for binary package installs.
The long undocumented remapping of
Rf_fround() in header ‘Rmath.h’ is now formally
trunc() in the
‘Rmath.h’ header has been disabled in C++ code (it has caused
getParseData() truncated the imaginary part of
complex number constants. (Reported by Yihui Xie.)
dbeta(x, a, b) with
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
cbind() did not handle
list objects correctly. (PR#15468)
replayPlot() now checks if it is replaying a plot
from the same session.
grid.raster() now give
error on an empty (zero-length) raster. (Reported by Ben North.)
min() did not handle
properly. (Reported by Magnus Thor Torfason.)
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
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,
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
source()) to segfault. (PR#15518)
The nonsensical use of
nmax = 1 in
unique() is now silently ignored.
qcauchy(p, *) is now fully accurate even when p is
very close to 1. (PR#15521)
valideta() functions in the
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
longer causes the window to close. (PR#15407)
Improved handling of edge cases in
HTML display of results from
?? sometimes contained badly constructed links.
c() and related functions such as
converted raw vectors to invalid logical vectors. (PR#15535)
(Windows only) When a call to
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.)
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
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)
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).
Sys.setlocale to set
"C" (to restore the sane behavior) no longer gives a
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).
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)
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
strptime() could fail. An example was French on
OS X, where juin is abbreviated to jui and partially
juillet. Similarly for weekday names.
pbeta(x, a, b, log.p = TRUE) sometimes underflowed to
zero for very small and very differently sized
approxfun() now handle infinite
values with the
"constant" method. (PR#15655)
stripchart() again respects reversed limits in
The ‘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
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
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.
format(lst) now also works when the list
lst has non-vector elements.
tools::getVignetteInfo() function has been added
to give information about installed vignettes.
assertCondition(), etc. utilities in tools, useful
Profiling now records non-inlined calls from byte-compiled
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.int() give more explicit error
messages if called with invalid (e.g.
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
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
the result, to avoid misuse creating invalid objects as in
PR#15303. A warning is given if a class is discarded.
npk has been copied from MASS to
allow more tests to be run without recommended packages being
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
to control the display of individual terms in the plot.
format() now supports
digits = 0, to
nsmall decimal places.
There is a new read-only
par() parameter called
"page", which returns a logical value indicating whether
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
NULL components in the replacement to be retained,
instead of causing corresponding components to be deleted.
tools::pkgVignettes() gains argument
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
file is not found. (Although
not from GNU, OpenCSW on Solaris installs it as
R CMD build (with the internal
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
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
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
R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-1.7.0on a Linux system and record that value rather than the frequently-changing full path such as ‘/usr/lib/jvm/java-1.7.0-openjdk-188.8.131.52.x86_64’.
Rscript -e requires a non-empty
argument for consistency with Unix versions of R. (Also
Rterm -e and
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
packages which are used in
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
The macros used for the texinfo manuals have been changed to
work better with the incompatible changes made in
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.
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
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.
applyClosure are now protected
against package code supplying an invalid
namespace argument to
package.skeleton() is now formally deprecated and will be
removed in R 3.1.0.
plclust() is deprecated: use the
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)
file.info() failed on root directories unless
the path was terminated with an explicit
regmatches<-() replacement function mishandled
results coming from
The help for
representation() still suggested the deprecated argument
R CMD config failed in an installed build of R
3.0.1 (only) when a sub-architecture was used. (Reported by
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
(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
qr.coef() and related functions did not properly coerce
real vectors to complex when necessary. (PR#15332)
ftable(a) now fixes up empty
that the result is printable.
package.skeleton() was not starting its search for
function objects in the correct place if
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)
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
: operator. (Found by Radford Neal; PR#15358,
NULL rather than omitting
components as documented. (Found by Radford Neal; PR#15360)
silent = TRUE could break a process that uses
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
closeStderr functions have gained the
round() now raise an
error if a single named argument is not named
deparse() now deparses raw vectors in a form that
is syntactically correct. (PR#15369)
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)
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
the last second before the epoch could not be converted from
POSIXct. (Reported by Bill Dunlap.)
add1.glm() miscalculated F-statistics when df > 1. (Bill
stem() now discards infinite inputs rather than
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.
strptime() now handles %W fields with value
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).
+ on a logical vector did not coerce to
integer, although unary
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 error reports misplaced the caret pointing out the bad token.
(Windows only) Starting R with
R (instead of
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)
x is a symbol,
is.vector(x, "name") now
should be synonyms. (Reported by Hervé Pagès.)
R CMD rtags works on platforms (such as OS X)
with a XSI-conformant shell command
is.unsorted(NA) returns false as documented (rather than
R CMD LINK did not know about sub-architectures.
system2() are better protected
against users who misguidedly have spaces in the temporary
edit() are now more likely to
work on file paths containing spaces. (Where external utilities
are used, not the norm on Windows nor in
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.
system2() now respects specifying
stderr as files if called from
x11() device whilst
identify() is in progress no longer hangs R. (PR#15253)
list.dirs(full.names = FALSE) was not implemented.
format() sometimes added unnecessary spaces.
all.equal(check.names = FALSE) would ignore the request
to ignore the names and would check them as attributes.
The symbol set by
was not respected in some locales. (PR#15435)
mcMap() was not exported by package
TukeyHSD objects did not balance
dev.flush() calls on multi-page plots.
ind argument (like
mcparallel has a new argument
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
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
ylim (and hence of
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
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
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
tz argument and not
"GMT" as documented
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
contain illegal multibyte strings (PR#15247).
Profiling of built-in functions with
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).
sep a character vector of length
greater than one and more than one argument was using separators
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
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,
not record information correctly, so replaying a graph (e.g. by
copying it to another device) would fail. (PR#15271)
dirname() with the
"" (which was being used in packages, despite
not being a file path) could have caused a segfault.
dirname("") is now
"" rather than
supsmu() could read/write outside its input vectors
for very short inputs (seen in package rms for
n = 4).
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
In R 3.0.0, when
help() found multiple pages with
the same alias, the HTML display of all the selections was not
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
lsfit() produced an incorrect error message when
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)
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.
Packages 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
ulimit in a
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
FALSE as before).
There is a new option,
.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
This is not intended for routine use, but can be very helpful in finding segfaults in package code.
layout(), the limits on the grid size have been
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
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
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
NaN are silently
Previously the behaviour was device-dependent.
Setting graphical parameters
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
as.tclObj() has been extended to handle raw vectors.
Previously, it only worked in the other direction.
(Contributed by Charlie Friedemann, PR#14939.)
been added, to allow generation of in-text citations from
"bibentry" objects. A
cite() function may be added
sort() method has been added for
bibstyle() function now defaults to setting the
default bibliography style. The
has been added to report the name of the current default style.
scatter.smooth() now has an argument
pass arguments to
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
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
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.
[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.)
uniroot() no longer use a
shared parameter object across calls. (
optim() with numerical derivatives
still do, as documented.)
all.equal() method for date-times is now
documented: times are regarded as equal (by default) if they
differ by up to 1 msec.
unique() gain a
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.
rwilcox() now return integer (not double) vectors. This
halves the storage requirements for large simulations.
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’.
forwardsolve()) are now
internal functions, for speed and support for large matrices.
More matrix algebra functions (e.g.
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.
splinefun() now return a
wrapper to an internal function in the stats namespace
rather than a
.Call() call. This is more
likely to work if the function is saved and used in a different
.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
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.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
(“is distributed as”) in plotmath.
domain = NA is accepted by
ngettext(), analogously to
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
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.
getRefClass() now return
class generator functions, similar to
still with the reference fields and methods as before
(suggestion of Romain Francois).
bitwXor(), using the internal
interfaces previously used for classes
bitwShiftR() for shifting bits
in elements of integer vectors.
"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
dir()) gains a new optional
no.. which allows to exclude
".." from listings.
Multiple time series are also of class
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.
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
a further such argument) needs a
length() method (which the
documented arguments never do). (Requested by Hervé Pagès; with a
.onDetach() is supported as an alternative to
.Last.lib, this does not need to
be exported from the package's namespace.
srcfile argument to
parse() may now be a
character string, to be used in error messages.
format() method for
ftable objects gains
method argument, propagated to
print(), allowing more compact output, notably for LaTeX
formatting, thanks to Marius Hofert.
utils::process.events() function has been added
to trigger immediate event handling.
Sys.which() now returns
NA inputs (related to PR#15147).
print() method for class
fewer trailing spaces (wish of PR#15124).
Also print output from
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,
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
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
untar() has a new argument
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.
parse() function has a new parameter
keep.source, which defaults to
Rprof() now optionally records information
at the statement level, not just the function level.
Rprof() function now quotes function names in
in its output file on Windows, to be consistent with the quoting
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.
options(stringsAsFactors = FALSE),
replications() now automatically convert character
vectors to factors without a warning.
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.
utils::packageName() has been added as
a lightweight version of
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.
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
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
On Windows, the device name for bitmap devices as reported
.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.
done at the beginning of the session if not already set.
(Suggestion of Bill Dunlap.)
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.
match()) or because other limits (e.g. of character strings
or matrix dimensions) would be exceeded or the operations would be
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
dist() can produce dissimilarity objects for more
than 65536 rows (but for example
hclust() cannot process
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.
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.
.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.
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
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
.Call calls copied from
earlier versions of R may no longer work – but they were never
part of the API.
.Call() calls in package base have been
solve() makes fewer copies, especially when
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
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
@<- operator is now implemented as a primitive,
which should reduce some copying of objects when used. Note that
the operator object must now be in package base: do not try
to import it explicitly from package methods.
The transitional support for installing packages without
namespaces (required since R 2.14.0) has been removed.
R CMD build will still add a namespace, but a
.First.lib() function will need to be converted.
R CMD INSTALL no longer adds a namespace (so
installation will fail), and a
.First.lib() function in a
package will be ignored (with an installation warning for now).
As an exception, packages without a ‘R’ directory and no ‘NAMESPACE’ file can still be installed.
Packages can specify in their ‘DESCRIPTION file’ a line like
Biarch: yesto be installed on Windows with --force-biarch.
Package vignettes can now be processed by other engines
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
File ‘etc/Makeconf’ makes more use of the macros
the compiler in use can be changed by setting just these (and if
necessary the corresponding flags and
FLIBS) in file
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
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’
R CMD check warns if it finds them.
R CMD check now does some checks on functions
defined within reference classes, including of
R CMD check --as-cran notes assignments to the
global environment, calls to
data() which load into the
global environment, and calls to
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
including options, can be specified via the environment
tools::massageExamples() is better protected against
packages which re-define base functions such as
get() and so can cause
R CMD check to fail when
R CMD javareconf has been enhanced to be more
similar to the code used by
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
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.
ENCODING argument to
.C() is defunct.
.Internal(eval.with.vis) non-API function has
Support for the converters for use with
.C() has been
removed, including the oft misused non-API header
The previously deprecated uses of
array() with a
dim argument and
tapply() with a 0-length
INDEX list are now errors.
Translation packages are defunct.
rep.int() on a pairlist or
other non-vector object is now an error.
Several non-API entry points have been transferred to
R_zeroin2) or replaced by different non-API
entry points (e.g.
The ‘internal’ graphics device invoked by
.Call("R_GD_nullDevice", package = "grDevices") has
been removed: use
pdf(file = NULL) instead.
.Fortran() entry point
"dqrls" which has
not been used by R since version 2.15.1 is no longer available.
traceOff() in package
methods are now defunct.
CRAN.packages() is finally defunct.
col2rgb(0) is defunct: use
The long-defunct functions
zip.file.extract() have been removed entirely (but are
still documented in the help system).
dataPath argument to
attachNamespace() has been removed.
grid.prompt() has been removed: use
intensities component is no
longer returned by
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.
keep.source argument to
require() is defunct. This option needs to be set
at install time.
is.real() has been moved to ‘defunct’ and the
maxRasters argument of
pdf() (unused since
R 2.14.0) has been removed.
fontsmooth argument has been removed from
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
deprecated: only the public versions without the dot have ever
been in the API.
In a package's ‘DESCRIPTION’ file,
License: X11is deprecated, since it includes ‘Copyright (C) 1996 X Consortium’ which cannot be appropriate for a current R package. Use ‘MIT’ or ‘BSD_2_clause’ instead.
The C code underlying base graphics has been migrated to the
graphics package (and hence no longer uses
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
.External() calls to the
(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
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
related to processes and threads it spawns.
mcparallel() has a new argument
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
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’.
.C() is now an error.
.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_I now have
size_t to allow them to work
with longer vectors on 64-bit platforms. Code using them should
A few recently added C entry points were missing the
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
PACKAGE = "" is now an error in
.C() etc calls:
it was always contrary to the documentation.
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
hsv2rgb have been
migrated to package grDevices and so are no longer available.
R_GE_version has been increased to
name2col removed (use
R_GE_str2col instead). R
internal colour codes are now defined using the typedef
REPROTECT macro now checks that the protect index
Several non-API entry points no longer used by R have been
removed, including the Fortran entry points
rg, and the C
.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
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
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
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 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
make pdf and
make install-pdf now make
and install the full reference index (including all base and
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
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
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.
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
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
LINPACK = TRUE but not in
the default case.
La.svd() accepts logical matrices (as documented, and
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
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
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
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
pf() calls, such as
pt(45, df=5000, lower.tail=FALSE,
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
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
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