Abstract
The ‘CHANGES IN R 3.6.2’ article from the 2019-2 issue.CHANGES IN R 3.6.2
NEW FEATURES
runmed(x, *) gains a new option na.action
determining how to handle NaN or NA
in x.dotchart() gains new options ann,
xaxt, frame.plot and log.INSTALLATION on a UNIX-ALIKE
configure: this is safer with LTO builds and allows the
detection to be overridden – see file config.site.gcc -fno-common (the expected default for
gcc 10.x).C-LEVEL FACILITIES
installTrChar (which is nowadays is wrapped by
installChar) is defined in Rinternals.h.
(Neither are part of the API.)PACKAGE INSTALLATION
Rconfig.h contains the value of
FC_LEN_T deduced at installation which is used by the
prototypes in headers R_ext/BLAS.h and
R_ext/Lapack.h but to avoid extensive breakage this is only
exposed when USE_FC_LEN_T is defined. If a package’s C/C++
calls to BLAS/LAPACK allow for the ‘hidden’ arguments used by most
Fortran compilers to pass the lengths of Fortran character arguments,
define USE_FC_LEN_T and include Rconfig.h
(possibly via R.h) before including
R_ext/BLAS.h or R_ext/Lapack.h.USE_FC_TO_LINK= in
src/Makevars[.win] and using
$(SHLIB_OPENMP_FFLAGS) as part of PKG_LIBS.
The known reason for doing so is a package which uses Fortran (only)
OpenMP on a platform where the Fortran OpenMP runtime is incompatible
with the C one (e.g. gfortran 9.x with
clang).UTILITIES
R CMD check has a new option to mitigate checks leaving
files/directories in /tmp. See the ‘R Internals’ manual –
this is part of –as-cran.Windows
DEPRECATED AND DEFUNCT
R CMD config for F77,
FCPIFCPLAGS, CPP, CXXCPP and
CXX98 and similar is deprecated. (CPP is found
from the system make and may well not be set.) Use
$CC -E and $CXX -E instead of CPP
and CXXCPP.BUG FIXES
runmed(x, *) when x contains missing
values now works consistently for both algorithm="Stuetzle"
and "Turlach", and no longer segfaults for
"Turlach", as reported by Hilmar Berger.apply(diag(3), 2:3, mean) now gives a helpful error
message.dgamma(x, shape, log=TRUE) now longer overflows to
Inf for shape < 1 and very small x, fixing
, reported by Jonathan Rougier.options(str = .) is correctly initialized at package
utils load time, now. A consequence is that str()
in scripts now is more consistent to interactive use, e.g., when
displaying function(**) argument lists.as.numeric(<call>) now gives correct error
message.ls.str() no longer wrongly shows
"<missing>" in rare cases.pchisq(<LRG>, <LRG>, ncp=100) no longer
takes practically forever in some cases. Hence ditto for corresponding
qchisq() calls.x %% L for finite x no longer returns
NaN when L is infinite, nor suffers from
cancellation for large finite L, thanks to Long Qu’s .
Analogously, x %/% L and L %/% x suffer less
from cancellation and return values corresponding to limits for large
L.grepl(NA, *) now returns logical as
documented.options(warn=1e11) is an error now, instead of later
leading to C stack overflow because of infinite recursion.R_tryCatch no longer transfers control for all
conditions. Reported and patch provided by Lionel Henry in .format(object.size(.), digits=NULL) now works, fixing
reported by Jonathan Carroll.get_all_vars(f, d) now also works for cases, e.g. where
d contains a matrix. Reported by Simon Wood in 2009 and
patch provided by Ben Bolker in . Additionally, it now also works when
some variables are data frames, fixing , reported by Patrick
Breheny.barplot() could get spacings wrong if there were
exactly two bars . Patch by Michael Chirico.power.t.test() works in more cases when returning
values of n smaller than 2.dotchart(*, pch=., groups=.) now works better. Reported
by Robert and confirmed by Nic Rochette in .canCoerce(obj, cl) no longer assumes
length(class(obj)) == 1.plot.formula(*, subset = *) now also works in a
boundary case reported by Robert Schlicht (TU Dresden).readBin() and writeBin() of a
rawConnection() now also work in large cases, thanks to a
report and proposal by Taeke Harkema in .CHANGES IN R 3.6.1
INSTALLATION on a UNIX-ALIKE
libNN is
overridden for derivatives of Debian Linux, some of which have started
to have a /usr/lib64 directory. (E.g. Ubuntu 19.04.) As
before, it can be specified in config.site.UTILITIES
R CMD config knows the values of AR and
RANLIB, often set for LTO builds.DEPRECATED AND DEFUNCT
.Fortran() is
formally deprecated and gives a non-portability warning. (It has long
been strongly discouraged in ‘Writing R Extensions’.)BUG FIXES
menuInstallPkgs() works again, thanks to Len Weil’s and
Duncan Murdoch’s .R CMD check on data() fixing thanks to
Duncan Murdoch.quasi(*, variance = list(..)) now works more
efficiently, and should work in all cases fixing . Further,
quasi(var = mu(1-mu)) and
quasi(var = "mu ^ 3") now work, and
quasi(variance = "log(mu)") now gives a correct error
message.boxplot(y ~ f, horizontal=TRUE) now produces correct x-
and y-labels.rbind.data.frame() allows to keep
<NA> levels from factor columns () via new option
factor.exclude. Additionally, it works in one more case
with matrix-columns which had been reported on 2017-01-16 by Krzysztof
Banas.R CMD check, fixing thanks to Xavier Robin.functions with a user defined print.function,
thanks to Bill Dunlap’s report.writeClipboard(.., format = <n>) now
does correctly pass format to the underlying C code, thanks
to a bug report (with patch) by Jenny Bryan.as.data.frame() treats 1D arrays the same as vectors,
.smoothEnds(x, *) working with
NAs (towards runmed() working in that case, in
the next version of R).vcov(glm(<quasi>), dispersion = *) works
correctly again, fixing thanks to Pavel Krivitsky.R CMD INSTALL of binary packages on Windows now works
also with per-directory locking.R CMD INSTALL and install.packages() on
Windows are now more robust against a locked file in an earlier
installation of the package to be installed. The default value of option
install.lock on Windows has been changed to
TRUE.readline is active), only expand
tilde (~) file names starting with a tilde, instead of
almost all tildes.*.Rd) files, item [..]
is no longer treated specially when rendered in LaTeX and hence pdf, but
rather shows the brackets in all cases.CHANGES IN R 3.6.0
SIGNIFICANT USER-VISIBLE CHANGES
save(),
serialize(), saveRDS(),
compiler::cmpfile()). Serialized data in format 3 cannot be
read by versions of R prior to version 3.5.0. Serialization format
version 2 is still supported and can be selected by
version = 2 in the save/serialization functions. The
default can be changed back for the whole R session by setting
environment variables R_DEFAULT_SAVE_VERSION and
R_DEFAULT_SERIALIZE_VERSION to 2. For maximal
back-compatibility, files vignette.rds and
partial.rdb generated by R CMD build are in
serialization format version 2, and resave by default produces files in
serialization format version 2 (unless the original is already in format
version 3).sample(), for instance) has been
changed. This addresses the fact, pointed out by Ottoboni and Stark,
that the previous method made sample() noticeably
non-uniform on large populations. See for a discussion. The previous
method can be requested using RNGkind() or
RNGversion() if necessary for reproduction of old results.
Thanks to Duncan Murdoch for contributing the patch and Gabe Becker for
further assistance. The output of RNGkind() has been
changed to also return the ‘kind’ used by sample().NEW FEATURES
Sys.setFileTime() has been vectorized so arguments
path and time of length greater than one are
now supported.
axis() gets new option gap.axis = NA
for specifying a multiplication factor for the minimal “gap” (distance)
between axis labels drawn. Its default is 1 for labels
parallel to the axis, and 0.25 for perpendicular
ones. Perpendicular labels no longer overlap, fixing bug .
The default method of plot() gains new arguments
xgap.axis = NA and ygap.axis = NA to be passed
to the x– and y– axis(.., gap.axis=*) calls.
removeSource() now works not only for functions but
also for some language objects.
as.call(), rep.int(),
rep_len() and nchar() dispatch
internally.
is(object, class2) looks for class2 in
the calling namespace after looking in the namespace of
class(object).
extendrange(.., f) with a length-2 f
now extends separately to the left and the right.
lengths() dispatches internally to S4
methods.
download.file() on Windows now uses
URLdecode() to determine the file extension, and uses
binary transfer (mode = "wb") also for file extension
.rds. The help page for download.file() now
contains the same information on all platforms.
Setting C locale for collation via
environment variables LC_ALL and LC_COLLATE
and via a call to Sys.setlocale() now takes
precedence over environment variable R_ICU_LOCALE.
There is a new function, nullfile(), to give the
file name of the null system device (e.g., /dev/null) on
the current platform.
There are two new options, keep.parse.data and
keep.parse.data.pkgs, which control whether parse data are
included into sources when keep.source or
keep.source.pkgs is TRUE. By default,
keep.parse.data.pkgs is now FALSE, which
changes previous behavior and significantly reduces space and time
overhead when sources are kept when installing packages.
In rapply(x, ..), x can also be
“list-like” and of length .
trimws() gets new optional whitespace
argument, allowing more extensive definitions of “space”, such as
including Unicode spaces (as wished in ).
weighted.mean() no longer coerces the weights to a
double/numeric vector, since sum() now handles integer
overflow. This makes weighted.mean() more polymorphic and
endomorphic, but be aware that the results are no longer guaranteed to
be a vector of type double.
When loading namespaces, S3 method registrations which overwrite
previous registrations are now noted by default (using
packageStartupMessage()).
compiler::cmpfile() gains a version
argument, for use when the output file should be saved in serialization
format 2.
The axis labeling in the default method of pairs()
may now be toggled by new options horOdd and
verOdd.
(Not Windows nor macOS.) Package tcltk now supports an
environment variable R_DONT_USE_TK which if set disables Tk
initialization. This is intended for use to circumvent errors in loading
the package, e.g. with recent Linux running under an address
sanitizer.
The numeric method of all.equal() gets
optional arguments countEQ and formatFUN. If
countEQ is true, the mean error is more sensible when many
entries are ual.
outer(x,y, FUN = "*") is more efficient using
tcrossprod(u,v) instead of
u %*% t(v).
vcov(<mlm>) is more efficient via new optional
arguments in summary.mlm().
The default method of summary() gets an option to
choose the kind of quantile()s to use; wish of
.
Fitting multiple linear models via lm()
does work with matrix offsets, as suggested in .
The new functions mem.maxVSize() and
mem.maxMSize() allow the maximal size of the vector heap
and the maximal number of nodes allowed in the current R
process to be queried and set.
news() gains support for NEWS.md
files.
An effort has been started to have our reference manuals, i.e.,
all help pages. show platform-independent information (rather than
Windows or Unix-alike specifics visible only on that platform).
Consequently, the Windows version of X11() /
x11() got identical formal arguments to the Unix
one.
sessionInfo()$running has been factored out in a new
variable osVersion.
slice.index() now also works for multi-dimensional
margins.
untar() used with an external tar
command assumes this supports decompression including xz
and automagically detecting the compression type. This has been true of
all mainstream implementations since 2009 (for GNU tar,
since version 1.22): older implementations are still supported
via the new argument support_old_tars whose
default is controlled by environment variable
R_SUPPORT_OLD_TARS. (It looks like NetBSD and OpenBSD have
‘older’ tar commands for this purpose.)
The new function asplit() allow splitting an array
or matrix by its margins.
New functions errorCondition() and
warningCondition() provide a convenient way to create
structured error and warning objects. .Deprecated() now
signals a warning of class "deprecatedWarning", and
.Defunct() now signals an error of class
"defunctError".
Many ‘package not found’ errors are now signaled as errors of
class "packageNotFoundError".
As an experimental feature, when loadNamespace()
fails because the requested package is not available the error is
initially signaled with a retry_loadNamespace restart
available. This allows a calling handler to try to install the package
and continue.
S3method() directives in NAMESPACE can
now also be used to perform delayed S3 method
registration.
Experimentally, setting environment variable
_R_CHECK_LENGTH_1_LOGIC2_ will lead to warnings (or errors
if the variable is set to a ‘true’ value) when &&
or || encounter and use arguments of length more than
one.
Added "lines" and "chars" coordinate
systems to grconvertX() and
grconvertY().
getOption() is more efficient notably for the rare
case when called with two arguments, from several contributors in
.
In .col(dim) and .row(dim),
dim now may also be an integer-valued
"double".
sQuote() and dQuote() get an explicit
q argument with obvious default instead of using
getOption("fancyQuotes") implicitly and
unconditionally.
unzip() can list archives with comments and with
spaces in file names even using an external unzip
command.
Command line completion has a new setting
rc.settings(dots = FALSE) to remove ... from
the list of possible function arguments.
library() no longer checks packages with compiled
code match R.version$platform. loadNamespace()
never has, and increasingly the ‘canonical name’ does not reflect the
important characteristics of compiled code.
The primitive functions drop() and
unclass() now avoid duplicating their data for atomic
vectors that are large enough, by returning ALTREP wrapper
objects with adjusted attributes. R-level assignments to change
attributes will also use wrapper objects to avoid duplicating data for
larger atomic vectors. R functions like structure() and
unname() will therefore not duplicate data in these
settings. Generic vectors as produced by list() are not yet
covered by this optimization but may be in due course.
In formals(), envir becomes an optional
argument instead of being hardwired.
Instead of signalling an error for an invalid S4 object
x, str(x) now gives a warning and subsequently
still shows most parts of x, e.g., when slots are
missing.
gamma(x) and lgamma(x) no longer warn
when correctly returning Inf or underflowing to zero. This
helps maximum likelihood and similar computations.
convertColor() is now vectorized, so a lot faster
for converting many colours at once. The new argument
vectorized to colorConverter() ensures that
non-vectorized colour converters still work. (Thanks to Brodie
Gaslam.)
download.file() and url() get new
argument headers for custom HTTP headers, e.g., allowing to
perform basic http authentication, thanks to a patch contributed by
Gábor Csárdi.
File-based connection functions file(),
gzfile(), bzfile() and xzfile()
now signal an error when used on a directory.
For approx(), splinefun() etc,
a new setting ties = c("ordered", <fun>) allows
skipping the sorting and still treat ties.
format(x) gives a more user friendly error message
in the case where no method is defined. A minimal method is provided in
format.default(x) when isS4(x) is
true.
which(x) now also works when x is a
long vector, thanks to Suharto Anggono’s . NB: this may
return a double result, breaking the previous guarantee of an integer
result.
seq.default() is more careful to return an
integer (as opposed to double) result when its
arguments are large and/or classed objects; see comment #9 of Suharto
Anggono’s .
The plot() method for lm and
glm fits, plot.lm(), gains a new option
iter.smooth with a default of 0 for binomial
fits, no longer down-weighting when smoothing the residuals.
zip() passes its list of files via standard
input to the external command when too long for the command line (on
some platforms).
data() gains an overwrite
argument.
t.test() now also returns the standard error (in
list component stderr).
model.matrix(*, contrasts.arg = CC) now warns about
invalid contrasts.args.
Performance of substr() and substring()
has been improved.
stopifnot() has been simplified thanks to Suharto
Anggono’s proposals to become considerably faster for cheap
expressions.
The default ‘user agent’ has been changed when accessing
http:// and https:// sites using
libcurl. (A site was found which caused
libcurl to infinite-loop with the previous
default.)
sessionInfo() now also contains
RNGkind() and prints it when it differs from the default;
based on a proposal and patch by Gabe Becker in . Also,
RNGversion(getRversion()) works directly.
library() and require() now allow more
control over handling search path conflicts when packages are attached.
The policy is controlled by the new conflicts.policy
option.
barplot() gets a formula method, thanks to a patch
proposal by Arni Magnusson in .
pmax() and pmin(x) now also work for
long vectors, thanks to Suharto Anggono’s .
bxp() now warns when omitting duplicated
arguments.
New hcl.colors() function to provide wide range of
HCL-based colour palettes with much better perceptual properties than
the existing RGB/HSV-based palettes like rainbow(). Also a
new hcl.pals() function to list available palette names for
hcl.colors().
Contributed by Achim Zeileis.
The default colours for image() and
filled.contour() are now based on
hcl.colors().
The palette-generating functions rainbow(),
gray.colors(), etc. get a new rev argument to
facilitate reversing the order of colors.
New str2lang() and str2expression() as
streamlined versions of parse(text=., keep.source=FALSE)
allow to abstract typical call constructions, e.g., in
formula manipulations. (Somewhat experimental)
Add update_PACKAGES() for incrementally updating a
package repository index, instead of rebuilding the index from scratch.
Thanks to Gabe Becker in for the patch, based on part of his
switchr package.
INSTALLATION on a UNIX-ALIKE
The options selected for the C++ compiler default to the C++11 standard if supported, otherwise to the C++98 standard.
Visibility macros such as C_VISIBILITY can now be
user-set (including to empty), e.g. in
config.site.
Macro FCLIBS, which has sometimes been needed on
Solaris, has been renamed to FCLIBS_XTRA.
Macro F77 is always set to the value of
FC, so the latter should be set to user-select the Fortran
compiler for both fixed-form and free-form Fortran. In particular,
gfortran is now the first choice for F77, not
f95. Macros FFLAGS and FCFLAGS
remain distinct to allow for a compiler which needs a flag to select
free- or fixed-form Fortran (most use the source-file extension to
choose: .f is fixed-form and .f90 and
.f95 are free-form).
If only one of them is set, its value is used for both.
The special-casing of CFLAGS, CXXFLAGS
and FFLAGS for Intel compilers on Linux has been removed:
we do not have recent experience but the generic defaults now chosen are
the same as those previously special-cased for x86_64. If
necessary, override the defaults on the configure command
line or in file config.site.
Long-untested configure support for HP-UX and very
old versions of Linux has been removed.
configure –with-blas (without specifying a value)
includes OpenBLAS in its search (before ATLAS and a generic BLAS). This
follows recent versions of the ax_blas autoconf
macro.
The configure macro MAKEINFO has been
updated to TEXI2ANY.
Support for make install-strip has been
enhanced.
PACKAGE INSTALLATION
Source package installation is by default ‘staged’: the package
is installed into a temporary location under the final library directory
and moved into place once the installation is complete. The benefit is
that partially-installed packages are hidden from other R sessions. The
overall default is set by environment variable
R_INSTALL_STAGED. R CMD INSTALL has new
options –staged-install and
–no-staged-install, and packages can use the
StagedInstall field in their DESCRIPTION file
to opt out. (That opt-out is a temporary measure which may be withdrawn
in future.)
Staged installation requires either –pkglock or
–lock, one of which is used by default.
The interpretation of source code with extension .f
is changing. Previously this denoted FORTRAN 77 code, but current
compilers no longer have a FORTRAN 77 mode and interpret it as
‘fixed-form’ Fortran 90 (or later where supported) code. Extensions
.f90 and .f95 continue to indicate ‘free-form’
Fortran code. Legal FORTRAN 77 code is also legal fixed-form Fortran 9x;
however this change legitimizes the use of later features, in particular
to replace features marked ‘obsolescent’ in Fortran 90 and ‘deleted’ in
Fortran 2018 which gfortran 8.x and later warn
about.
Packages containing files in the src directory with
extensions .f90 or .f95 are now linked using
the C or C++ compiler rather than the Fortran 9x compiler. This is
consistent with fixed-form Fortran code and allows mixing of C++ and
free-form Fortran on most platforms. Consequentially, a package which
includes free-form Fortran 9x code which uses OpenMP should include
SHLIB_OPENMP_CFLAGS (or the CXXFLAGS version
if they also include C++ code) in PKG_LIBS rather than
SHLIB_OPENMP_FCFLAGS — fortunately on almost all current
platforms they are the same flag.
Macro PKG_FFLAGS will be used for the compilation of
both fixed-form and free-form Fortran code unless
PKG_FCFLAGS is also set (in src/Makevars or
src/Makevars.win).
The make macro F_VISIBILITY is now preferred for
both fixed-form and free-form Fortran, for use in
src/Makevars and similar.
R CMD INSTALL gains a new option –strip
which (where supported) strips installed shared object(s): this can also
be achieved by setting the environment variable
_R_SHLIB_STRIP_ to a true value. The new option
–strip-lib attempts stripping of static and shared
libraries installed under lib.
These are most useful on platforms using GNU binutils
(such as Linux) and compiling with -g flags.
There is more support for installing UTF-8-encoded packages in a
strict Latin-1 locale (and probably for other Latin locales): non-ASCII
comments in R code (and NAMESPACE files) are worked around
better.
UTILITIES
R CMD check now optionally checks makefiles for correct
and portable use of the SHLIB_OPENMP_*FLAGS macros.R CMD check now evaluates Sexpr{}
expressions (including those in macros) before checking the contents of
Rd files and so detects issues both in evaluating the
expressions and in the expanded contents.R CMD check now lists missing packages separated by
commas and with regular quotes such as to be useful as argument in
calling install.packages(c(..)); from a suggestion by
Marcel Ramos.tools::Rd2latex() now uses UTF-8 as its default output
encoding.R CMD check now checks line endings of files with
extension .hpp and those under inst/include.
The check now includes that a non-empty file is terminated with a
newline. R CMD build will correct line endings in such
files.R CMD check now tries re-building all vignettes rather
than stopping at the first error: whilst doing so it adds ‘bookmarks’ to
the log. By default (see the ‘R Internals’ manual) it re-builds each
vignette in a separate process. It now checks for duplicated vignette
titles (also known as ‘index entries’): they are used as hyperlinks on
CRAN package pages and so do need to be unique.R CMD check has more comprehensive checks on the
data directory and the functioning of data()
in a package.R CMD check now checks autoconf-generated
configure files have their corresponding source files,
including optionally attempting to regenerate them on platforms with
autoreconf.R CMD build has a new option –compression
to select the compression used for the tarball.R CMD build now removes src/*.mod files on
all platforms.C-LEVEL FACILITIES
R_PreserveInMSet and
R_ReleaseFromMSet have been introduced to replace
UNPROTECT_PTR, which is not safe to mix with
UNPROTECT (and with PROTECT_WITH_INDEX).
Intended for use in parsers only.NAMEDMAX has been raised to 7 to allow further
protection of intermediate results from (usually ill-advised)
assignments in arguments to BUILTIN functions. Properly
written package code should not be affected.R_unif_index is now considered to be part of the C
API.R_GetCurrentEnv() allows C code to retrieve the current
environment.DEPRECATED AND DEFUNCT
compressed of untar() is
deprecated — it is only used for external tar commands
which increasingly for extraction auto-detect compression and ignore
their zjJ flags.var(f) and hence sd(f) now give an error
for factor arguments; they gave a deprecation warning since
R 3.2.3, .vignetteDepends() has been
deprecated (it called a function deprecated since Feb 2016), being
partly replaced by newly exported vignetteInfo().f77_f2c script has been removed: it no longer
sufficed to compile the .f files in R.make macros such as
CXX1X has been removed: use the CXX11 forms
instead.F77_VISIBILITY is deprecated in favour of
F_VISIBILITY.F77, FCPIFCPLAGS and
SHLIB_OPENMP_FCFLAGS are deprecated in favour of
FC, FPICFLAGS and
SHLIB_OPENMP_FFLAGS respectively.$.data.frame had become an expensive version of the
default method, so has been removed. (Thanks to Radford Neal for picking
this up and to Duncan Murdoch for providing a patch.)BUG FIXES
replayPlot(r) now also works in the same R session when
r has been “reproduced” from serialization, typically after
saving to and reading from an RDS file.substr() and substring() now signal an
error when the input is invalid UTF-8.file.copy() now works also when its argument
to is of length greater than one.mantelhaen.test() no longer suffers from integer
overflow in largish cases, thanks to Ben Bolker’s .setGeneric("foo") in a package no longer fails
when the enclosing environment of the implicit generic
foo() is .GlobalEnv.untar(file("<some>.tar.gz"), *) now gives a
better error message, suggesting to use gzfile()
instead.identify() incorrectly claimed
that the indices of identified points were returned in the order that
the points were selected. identify() now has a new argument
order to allow the return value to include the order in
which points were identified; the documentation has been updated.
Reported by Richard Rowe and Samuel Granjeaud.order(...., decreasing=c(TRUE, FALSE)) could fail in
some cases. Reported from StackOverflow via Karlprint.*(), thanks to Lionel Henry’s patches
in :
show() rather than print(), as with
auto-printing.[[<n>]]) of recursive
data structures are now printed correctly in complex cases.print() are now properly
forwarded to methods when printing lists, pairlists or attributes
containing S3 objects.srcref attributes if present.install.packages() with a length zero
pkgs argument now is a no-op ().unlist(x) now returns a correct factor
when x is a nested list with factor leaves, fixing and
.help(family) gives more details about
the aic component, thanks to Ben Bolker’s prompting.attributes and
‘attributes<-‘ now gives x as name of the
first and main argument which the implementation has been requiring,
fixing . For consistency, the first argument name is also changed from
obj to x for
‘mostattributes<-‘.strwidth() now uses par("font") as default
font face ().plot(<table>, log="x") no longer warns about
log.print() method for "htest" objects now
formats the test statistic and parameter directly and hence no longer
rounds to units before the decimal point. Consequently,
printing of t.test() results with a small number of digits
now shows non-large df’s to the full precision ().kruskal.test() and fligner.test() no
longer erroneously insist on numeric g group arguments
().print.aov() missed column names in the multivariate
case due to misspelling (reported by Chris Andrews).axis() now creates valid at locations also
for small subnormal number ranges in log scale plots.format.POSIXlt() now also recycles the
zone and gmtoff list components to full length
when needed, and its internal C code detects have_zone in
more cases. In some cases, this changes its output to become compatible
with format.POSIXct().detectCores() in package parallel
now detects processors in all processor groups, not just the group R is
running in (impacts particularly systems with more than 64 logical
processors). Reported by Arunkumar Srinivasan.socketSelect() would hang with more than 64
sockets, and hence parallel::clusterApplyLB() would hang
with more than 64 workers. Reported by Arunkumar Srinivasan.as(1L, "double") now does coerce ().lm.influence(), influence.measures(),
rstudent() etc now work (more) correctly for multivariate
models ("mlm"), thanks to (anonymous) stackoverflow
remarks.sample.int(2.9, *, replace=TRUE) again behaves as
documented and as in R < 3.0.0, namely identically to
sample.int(2, ..).convertColor() for chromatic adaptation;
thanks to Brodie Gaslam .Sexpr[stage=install]{..} to create an
Rd section no longer gives a warning in
R CMD check; problem originally posted by Gábor Csárdi,
then reported as with a partial patch by Duncan Murdoch.split.default() no longer relies on
[[<-(), so it behaves as expected when splitting an
object by a factor with the empty string as one of its levels. Thanks to
Brad Friedman for the report..Rd files are now more
reliable, thanks to a patch from Duncan Murdoch.numeric method for all.equal(), a
numeric scale argument is now checked to be positive and
allowed to be of length > 1. (The latter worked originally and with a
warning in recent years).OutDec
option setting when not equal to the default. Reported by Michael
Sannella.y is numeric and f a
factor, plot(y ~ f) nicely uses "y" and "f" as
y- and x-labels. The more direct boxplot(y ~ f) now does
too. The new argument ann = FALSE may be used to suppress
these.formatC(*, zero.print = "< 0.001") no
longer give an error and are further improved via new optional argument
replace.zero. Reported by David Hugh-Jones.methods::formalArgs("<fn>") now finds the same
function as formals("<fn>"), fixing Emil Bode’s
.seq() now avoids integer
overflow, thanks to the report and "cumsum" patch of Suharto Anggono’s
.sub() no longer loses encodings for non-ASCII
replacements ().formula(model.frame(frml, ..)) now returns
frml in all cases, thanks to Bill Dunlap. The previous
behavior is available as
DF2formula(<model.frame>).ar.ols() also returns scalar var.pred in
univariate case ().normalizePath() now treats NA path as
non-existent and normalizes it to NA.
file.access() treats NA file name as
non-existent. file.edit() and connection functions such as
file() now treat NA file names as errors.regularize.values() auxiliary of
approx(), splinefun() etc now warns again when
there are ties and the caller did not specify ties.
Further, it no longer duplicates x and y
unnecessarily when x is already sorted ().strtoi("", base) now gives NA on all
platforms, following its documentation. Reported by Michael
Chirico.setClassUnion(), if environment variable
_R_METHODS_SHOW_CHECKSUBCLASSES is set to true, the
internal .checkSubclasses() utility prints debugging info
to see where it is used.max.col(m) with an m of zero columns now
returns integer NA (instead of 1).axTicks() no longer returns small “almost zero” numbers
(in exponential format) instead of zero, fixing Ilario Gelmetti’s .isSymmetric(matrix(0, dimnames=list("A","b"))) is
FALSE again, as always documented.cairo_pdf graphics device (and other Cairo-based
devices) now clip correctly to the right and bottom border. There was an
off-by-one-pixel bug, reported by Lee Kelvin.as.roman(3) <= 2:4 and all other comparisons now
work, as do group "Summary" function calls such as
max(as.roman(sample(20))) and as.roman(NA).
(Partly reported by Bill Dunlap in .)reformulate("x", response = "sin(y)") no longer
produces extra back quotes, , and gains new optional argument
env.stdin with re-encoding
(R –encoding=enc < input) the code on a Unix-alike now
ensures that each converted input line is terminated with a newline even
if re-encoding fails.as.matrix.data.frame() now produces better strings from
logicals, thanks to from Gabe Becker.rowSums(),
rowMeans(), colSums() and
colMeans() is restricted to "x".match(x, tab) now works for long character
vectors x, thanks to by Andreas Kersting.selectMethod() is robust to ANY-truncation of method
signatures (thanks to Herve Pages for the report).CHANGES IN R 3.5.3
INSTALLATION on a UNIX-ALIKE
PACKAGE INSTALLATION
F_VISIBILITY as an alternative to
F77_VISIBILITY. This will become the preferred form in R
3.6.0.BUG FIXES
writeLines(readLines(fnam), fnam) now works as
expected, thanks to Peter Meissner’s .setClassUnion() no longer warns, but uses
message() for now, when encountering “non local” subclasses
of class members.stopifnot(exprs = T) no longer fails.CHANGES IN R 3.5.2
PACKAGE INSTALLATION
CXX_VISIBILITY analogous to
C_VISIBILITY (which several packages have been misusing for
C++ code) for the default C++ compiler (but not necessarily one used for
non-default C++ dialects like C++14).TESTING
tests/p-r-random-tests.R no longer fail occasionally as
they now randomly sample from “certified” random seeds.BUG FIXES
"glm" method of drop1() miscalculated
the score test (test="Rao") when the model contained an
offset.lm(y ~ 0) now have
a correctly dimensioned empty coefficient matrix; reported by Brett
Presnell.vcov(<empty mlm>) and hence
confint() now work (via a consistency change in
summary.lm()).confint(<multiple lm()>) now works correctly;
reported on R-devel by Steven Pav.quade.test() now also works correctly when its
arguments are not yet sorted along groups, fixing .pthread library where required (rather than relying on
OpenMP to provide it: configuring with –disable-openmp was
failing on some Linux systems).data.frame method for print(x) is fast
now also for large data frames x and got an optional
argument max, thanks to suggestions by Juan Telleria.hist() no longer integer overflows in very rare cases,
fixing .untar() ignored a character compressed
argument: however many external tar programs ignore the
flags which should have been set and automagically choose the
compression type, and if appropriate gzip or
bzip2 compression would have been chosen from the magic
header of the tarball.zapsmall(x) now works for more “number-like”
objects.R CMD INSTALL
now gets a warnOption = 1 argument and only sets
options(warn = warnOption) when that increases the warning
level ().R CMD check gets a warnOption = 1 argument and
uses the larger of that and getOption("warn"), also
allowing to be run with increased warning level.match() with length one x and
POSIXlt table gave a segfault ().makeCluster()).nextn(n) now also works for larger n and
no longer loops infinitely for e.g, n <- 214e7.cooks.distance() and rstandard() now work
correctly for multiple linear models ("mlm").polym() and corresponding lm() prediction
now also work for a boundary "vector" case fixing , reported by
Alexandre Courtiol.terms() could
segfault ().cut(rep(0, 7)) now works, thanks to Joey Reid and
Benjamin Tyner ().download.file(*, method = "curl", cacheOK = FALSE)
should work now on Windows, thanks to Kevin Ushey’s patch in .duplicated(<dataframe with ’f’>) now works, too,
thanks to Andreas Kersting’s ; ditto for
anyDuplicated().legend(*, cex = 1:2) now works less badly.print() method for POSIXct and
POSIXlt now correctly obeys
getOption("max.print"), fixing a long-standing typo, and it
also gets a corresponding optional max argument.<data frame>[TRUE, <new>] <- list(c1, c2)
now works correctly, thanks to Suharto Anggono’s and Emil Bode’s patch
in .seq.int(*, by=by, length=n) no longer wrongly “drops
fractional parts” when by is integer, thanks to Suharto
Anggono’s report .file() connections to
non-regular files (like sockets), as well as fifo() and
pipe() connections. Fixes , reported by Chris Culnane.CHANGES IN R 3.5.1
BUG FIXES
file("stdin") is no longer considered seekable.dput() and dump() are no longer truncating
when options(deparse.max.lines = *) is set.file argument of Rscript to include
space even when it is first on the command line.callNextMethod() uses the generic from the environment
of the calling method. Reported by Hervé Pagès with well documented
examples.optim(*, lower = c(-Inf, -Inf)) no longer warns (and
switches the method), thanks to a suggestion by John Nash.predict(fm, newdata) is now correct also for models
where the formula has terms such as splines::ns(..) or
stats::poly(..), fixing , based on a patch from Duncan
Murdoch.simulate.lm(glm(*, gaussian(link = <non-default>)))
has been corrected, fixing thanks to Alex Courtiol.unlist(x) no longer fails in some cases of nested empty
lists. Reported by Steven Nydick.qr.coef(qr(<all 0, w/ colnames>)) now works.
Reported by Kun Ren.deparse(x), dput(x) and
dump() now respect c()’s argument names
recursive and use.names, e.g., for
x <- setNames(0, "recursive"), thanks to Suharto
Anggono’s ..Renviron on Windows with Rgui is again by
default searched for in user documents directory when invoked
via the launcher icon. Reported by Jeroen Ooms.printCoefmat() now also works with explicit
right=TRUE.print.noquote() now also works with explicit
quote=FALSE.pairs(.., horInd=*, verInd=*)
now gets the correct order, thanks to reports by Chris Andrews and
Gerrit Eichner. Additionally, when horInd or
verInd contain only a subset of variables, all the axes are
labeled correctly now.agrep("..|..", .., fixed=FALSE) now matches when it
should, thanks to a reminder by Andreas Kolter.str(ch) now works for more invalid multibyte
strings.CHANGES IN R 3.5.0
SIGNIFICANT USER-VISIBLE CHANGES
.Call and similar).NEW FEATURES
UTILITIES
install.packages() for source packages now has the
possibility to set a ‘timeout’ (elapsed-time limit). For serial installs
this uses the timeout argument of system2():
for parallel installs it requires the timeout utility
command from GNU coreutils.R CMD check via environment variables
documented in the ‘R Internals’ manual.setRepositories(). This
changes the mapping for 6–8 used by
setRepositories(ind=).R CMD check now also applies the settings of
environment variables _R_CHECK_SUGGESTS_ONLY_ and
_R_CHECK_DEPENDS_ONLY_ to the re-building of
vignettes.R CMD check with environment variable
_R_CHECK_DEPENDS_ONLY_ set to a true value makes
test-suite-management packages available and (for the time being) works
around a common omission of from the VignetteBuilder
field.INSTALLATION on a UNIX-ALIKE
configure works harder to set additional flags in
SAFE_FFLAGS only where necessary, and to use flags which
have little or no effect on performance. In rare circumstances it may be
necessary to override the setting of SAFE_FFLAGS.expm1, hypot,
log1p and nearbyint are now required.configure sets a -std flag for the C++
compiler for all supported C++ standards (e.g.,
-std=gnu++11 for the C++11 compiler). Previously this was
not done in a few cases where the default standard passed the tests made
(e.g. clang 6.0.0 for C++11).C-LEVEL FACILITIES
MAYBE_REFERENCED, MAYBE_SHARED and
MARK_NOT_MUTABLE that should be used by package
C code instead NAMED or
SET_NAMED.ALTREP branch. This requires re-installing packages that
use compiled code.R_tryCatch,
R_tryCatchError, and R_UnwindProtect
functions.NAMEDMAX has been raised to 3 to allow protection of
intermediate results from (usually ill-advised) assignments in arguments
to BUILTIN functions. Package C code using
SET_NAMED may need to be revised.DEPRECATED AND DEFUNCT
Sys.timezone(location = FALSE) is defunct, and is
ignored (with a warning).methods:::bind_activation() is defunct now; it
typically has been unneeded for years. The undocumented ‘hidden’ objects
.__H__.cbind and .__H__.rbind in package
base are deprecated (in favour of cbind and
rbind).pythag() in Rmath.h has
been removed — the entry point has not been provided since R
2.14.0.BUG FIXES
printCoefmat() now also works without column
names.Ops() for the
"structure" class no longer cause infinite recursion when
the structure is not an S4 object.nlm(f, ..) for the case where f() has a
"hessian" attribute now computes correctly. ().NULL no
longer drops the argument from its formals.Rscript can now accept more than one argument given on
the #! line of a script. Previously, one could only pass a
single argument on the #! line in Linux."UTF-16LE". ()...0 now signals an error. When
..1 is used and ... is empty, the error
message is more appropriate.stopifnot(e, e2, ...) now evaluates the expressions
sequentially and in case of an error or warning shows the relevant
expression instead of the full stopifnot(..) call.path.expand() on Windows now accepts paths specified as
UTF-8-encoded character strings even if not representable in the current
locale. ()line(x, y) now correctly computes the medians of the
left and right group’s x-values and in all cases reproduces straight
lines.dim and dimnames now works.legend() when fill has multiple
values the first of which is NA (all colours used to
default to par(fg)). ()installed.packages() did not remove the cached value
for a library tree that had been emptied (but would not use the old
value, just waste time checking it).installed.packages(noCache = TRUE) incorrectly claimed it
would refresh the cache.aggregate(<data.frame>) no longer uses spurious
names in some cases. ()object.size() now also works for long vectors.packageDescription() tries harder to solve re-encoding
issues, notably seen in some Windows locales. This fixes the
citation() issue in .poly(<matrix>, 3) now works, thanks to prompting
by Marc Schwartz.readLines() no longer segfaults on very large files
with embedded ’0’ (aka ‘nul’) characters. ()ns() (package splines) now also works for a
single observation. interpSpline() gives a more friendly
error message when the number of points is less than four.dist(x, method = "canberra") now uses the correct
definition; the result may only differ when x contains
values of differing signs, e.g. not for 0-1 data.methods:::cbind() and methods:::rbind()
avoid deep recursion, thanks to Suharto Anggono via .^ (which previously gave a numeric matrix).pretty(x, n) for large n or large
diff(range(x)) now works better (though it was never meant
for large n); internally it uses the same rounding fuzz
(1e-10) as seq.default() — as it did up to 2010-02-03 when
both were 1e-7.R_check_class_and_super() and hence
R_check_class_etc() now also consider non-direct super
classes and hence return a match in more cases. This e.g., fixes
behaviour of derived classes in package .return calls
in on.exit expressions introduced by stack unwinding
changes in R 3.3.0.fisher.test(*, workspace = <n>) now may also
increase the internal stack size which allows larger problem to be
solved, fixing .length<-() on NULL (during the bootstrap
process).sys.on.exit() is now always evaluated in the right
frame. (From Lionel Henry.)seq.POSIXt(*, by = "<n> DSTdays") now should work
correctly in all cases and is faster. ().C() when returning a logical vector now always maps
values other than FALSE and NA to TRUE (as documented).x <- numeric(); x[1] <- character() now
signals an error ‘replacement has length zero’ (or a translation of
that) instead of doing nothing.mclapply(),
pvec() and mcparallel() (when
mccollect() is used to collect results) no longer leave
zombie processes behind.R CMD INSTALL <pkg> now produces the intended
error message when, e.g., the LazyData field is
invalid.as.matrix(dd) now works when the data frame
dd contains a column which is a data frame or matrix,
including a 0-column matrix/d.f. .mclapply(X, mc.cores) now follows its documentation and
calls lapply() in case mc.cores = 1 also in
the case mc.preschedule is false. ()aggregate(<data.frame>, drop=FALSE) no longer
calls the function on <empty> parts but sets corresponding results
to NA. (Thanks to Suharto Anggono’s patches in ).duplicated() method for data frames is now based on
the list method (instead of string coercion). Consequently
unique() is better distinguishing data frame rows, fixing
and . The methods for matrices and arrays are changed accordingly.names() on an S4 object derived from
"environment" behaves (by default) like calling
names() on an ordinary environment.read.table() with a non-default separator now supports
quotes following a non-whitespace character, matching the behavior of
scan().parLapplyLB and parSapplyLB have been
fixed to do load balancing (dynamic scheduling). This also means that
results of computations depending on random number generators will now
really be non-reproducible, as documented.l$"")
returns NULL.usage{ data(<name>, package="<pkg>") } no
longer produces R CMD check warnings.match.arg() more carefully chooses the environment for
constructing default choices, fixing as proposed by Duncan
Murdoch.! calls is now consistent with
deparsing unary - and + calls and creates code
that can be reparsed exactly; thanks to a patch by Lionel Henry in . (As
a side effect, this uses fewer parentheses in some other deparsing
involving ! calls.)CHANGES IN R 3.4.4
NEW FEATURES
Sys.timezone() tries more heuristics on Unix-alikes and
so is more likely to succeed (especially on Linux). For the slowest
method, a warning is given recommending that TZ is set to
avoid the search.parallel::detectCores(logical = FALSE) is ignored on
Linux systems, since the information is not available with virtualized
OSes.INSTALLATION on a UNIX-ALIKE
configure will use pkg-config to find the
flags to link to jpeg if available (as it should be for the
recently-released jpeg-9c and libjpeg-turbo).
(This amends the code added in R 3.3.0 as the module name in
jpeg-9c is not what that tested for.)DEPRECATED AND DEFUNCT
Sys.timezone(location = FALSE) (which was a stop-gap
measure for Windows long ago) is deprecated. It no longer returns the
value of environment variable TZ (usually a location).make macros such as
CXX1X is formally deprecated: use the CXX11
forms instead.BUG FIXES
power.prop.test() now warns when it cannot solve the
problem, typically because of impossible constraints. ()removeSource() no longer erroneously removes
NULL in certain cases, thanks to Dénes Tóth.nls(‘NO [mol/l]‘ ~ f(t)) and nls(y ~ a)
now work. (Partly from )R CMD build checks for GNU cp rather than
assuming Linux has it. ( says ‘Alpine Linux’ does not.)sum(<large ints>, <stuff>) is more
consistent. ()rf() and rbeta() now also work correctly
when ncp is not scalar, notably when (partly)
NA. ()is.na(NULL) no longer warns. ()R CMD INSTALL now correctly sets C++ compiler flags
when all source files are in sub-directories of src.CHANGES IN R 3.4.3
INSTALLATION on a UNIX-ALIKE
–with-internal-tzcode (the default on
macOS).R CMD javareconf has been updated to recognize the use
of a Java 9 SDK on macOS.BUG FIXES
raw(0) & raw(0) and raw(0) | raw(0)
again return raw(0) (rather than
logical(0)).intToUtf8() converts integers corresponding to
surrogate code points to NA rather than invalid UTF-8, as
well as values larger than the current Unicode maximum of
0x10FFFF. (This aligns with the current RFC3629.)... when the call contains ....utf8ToInt().range(c(TRUE, NA), finite = TRUE) and similar no longer
return NA. (Reported by Lukas Stadler.)attr(SSlogis, "initial") now
also works when the y values have exact minimum zero and is slightly
changed in general, behaving symmetrically in the y range.CHANGES IN R 3.4.2
NEW FEATURES
LC_ALL category in
Sys.setlocale() invalidates any cached locale-specific
day/month names and the AM/PM indicator for strptime() (as
setting LC_TIME has since R 3.1.0).tools::write_PACKAGES(rds_compress=)
has been changed to "xz" to match the compression used by
CRAN.c() and unlist() are now more efficient in
constructing the names(.) of their return value, thanks to
a proposal by Suharto Anggono. ()UTILITIES
R CMD check checks for and R CMD build
corrects CRLF line endings in shell scripts configure and
cleanup (even on Windows).INSTALLATION on a UNIX-ALIKE
-fopenmp and
-xopenmp but only the latter enables OpenMP so it is now
tried first.BUG FIXES
within(List, rm(x1, x2)) works correctly again,
including when List[["x2"]] is NULL.regexec(pattern, text, *) now applies
as.character(.) to its first two arguments, as
documented.write.table() and related functions,
writeLines(), and perhaps other functions writing text to
connections did not signal errors when the writes failed, e.g. due to a
disk being full. Errors will now be signalled if detected during the
write, warnings if detected when the connection is closed. ()rt() assumed the ncp parameter was a
scalar. ()menu(choices) with more than 10 choices which easily
fit into one getOption("width")-line no longer erroneously
repeats choices. ()length()<- on a pairlist succeeds. (https://stat.ethz.ch/pipermail/r-devel/2017-July/074680.html)quote(("n")) or R functions
are correctly printed again, where R 3.4.1 accidentally duplicated the
backslashes.names() for very large objects in
c() and unlist() now works, thanks to Suharto
Anggono’s patch proposals in .model.matrix(~1, mf) now gets the row names from
mf also when they differ from 1:nrow(mf),
fixing thanks to the suggestion by Sebastian Meyer.sigma(fm) now takes the correct denominator degrees of
freedom for a fitted model with NA coefficients. ()hist(x, "FD") no longer “dies” with a somewhat cryptic
error message when x has extreme outliers or
IQR() zero: nclass.FD(x) tries harder to find
a robust bin width in the latter case, and
hist.default(*, breaks) now checks and corrects a too large
breaks number. ()callNextMethod() works for ...
methods.qr.coef(qd, y) now has correct names also when
qd is a complex QR or stems from
qr(*, LAPACK=TRUE).options(device = *) to an invalid function no
longer segfaults when plotting is initiated. ()encodeString(<very large string>) no longer
segfaults. ()configure –enable-maintainer-mode without having installed
notangle (it was required in R 3.4.\[01\]).... calls the method by name
instead of .Method (for consistency with default dispatch),
and only attempts to pass non-missing arguments from the generic.readRDS(textConnection(.)) works again. ()(1:n)[-n] no longer segfaults for
n <- 2.2e9 (on a platform with enough RAM).x <- 1:2; tapply(x, list(x, x), function(x) "")[1,2]
now correctly returns NA. ()do_gc to the C interface
R_gc. This helps with reclaiming inaccessible
connections.help.search(topic) and ??topic matching
topics in vignettes with multiple file name extensions (e.g.,
*.md.rsp but not *.Rmd) failed with an error
when using options(help_type = "html").array(character(), 1) now gives (a 1D array with)
NA as has been documented for a long time as in the other
cases of zero-length array initialization and also compatibly with
matrix(character(), *). As mentioned there, this also fixes
.splineDesign(.., derivs = 4) no longer segfaults.fisher.test(*, hybrid=TRUE) now (again) will use the
hybrid method when Cochran’s conditions are met, fixing .CHANGES IN R 3.4.1
INSTALLATION on a UNIX-ALIKE
BUG FIXES
getParseData() gave incorrect column information when
code contained multi-byte characters. ()?stats::cor()
did not work. ()readRDS(url(....)) now works.R CMD Sweave again returns status = 0 on
successful completion..Rbuildignore were not being
ignored properly. ()file.mtime() no longer returns NA on Windows when the
file or directory is being used by another process. This affected
installed.packages(), which is now protected against
this.R CMD INSTALL Windows .zip file obeys
–lock and –pkglock flags.choose.files() function could return
incorrect results when called with multi = FALSE. ()aggregate(<data.frame>, drop = FALSE) now also
works in case of near-equal numbers in by. ()fourfoldplot() could encounter integer overflow when
calculating the odds ratio. ()parse() no longer gives spurious warnings when
extracting srcrefs from a file not encoded in the current locale. This
was seen from R CMD check with inst/doc/*.R
files, and check has some additional protection for such
files.print.noquote(x) now always returns its argument
x (invisibly).CHANGES IN R 3.4.0
SIGNIFICANT USER-VISIBLE CHANGES
(Unix-alike) The default methods for download.file()
and url() now choose "libcurl" except for
file:// URLs. There will be small changes in the format and
wording of messages, including in rare cases if an issue is a warning or
an error. For example, when HTTP re-direction occurs, some messages
refer to the final URL rather than the specified one. Those who use
proxies should check that their settings are compatible (see
?download.file: the most commonly used forms work for both
"internal" and "libcurl").
table() has been amended to be more internally
consistent and become back compatible to R 2.7.2 again. Consequently,
table(1:2, exclude = NULL) no longer contains a zero count
for <NA>, but useNA = "always" continues
to do so.
summary.default() no longer rounds, but its print
method does resulting in less extraneous rounding, notably of numbers in
the ten thousands.
factor(x, exclude = L) behaves more rationally when
x or L are character vectors. Further,
exclude = <factor> now behaves as documented for
long.
Arithmetic, logic (&, |) and
comparison (aka ‘relational’, e.g., <, ==)
operations with arrays now behave consistently, notably for arrays of
length zero. Arithmetic between length-1 arrays and longer non-arrays
had silently dropped the array attributes and recycled. This now gives a
warning and will signal an error in the future, as it has always for
logic and comparison operations in these cases (e.g., compare
matrix(1,1) + 2:3 and
matrix(1,1) < 2:3).
The JIT (‘Just In Time’) byte-code compiler is now enabled by
default at its level 3. This means functions will be compiled on first
or second use and top-level loops will be compiled and then run. (Thanks
to Tomas Kalibera for extensive work to make this possible.) For now,
the compiler will not compile code containing explicit calls to
browser(): this is to support single stepping from the
browser() call.
JIT compilation can be disabled for the rest of the session using
compiler::enableJIT(0) or by setting environment variable
R_ENABLE_JIT to 0.
xtabs() works more consistently with
NAs, also in its result no longer setting them to
0. Further, a new logical option addNA allows
to count NAs where appropriate. Additionally, for the case
sparse = TRUE, the result’s dimnames are
identical to the default case’s.
Matrix products now consistently bypass BLAS when the inputs have
NaN/Inf values. Performance of the check of
inputs has been improved. Performance when BLAS is used is improved for
matrix/vector and vector/matrix multiplication (DGEMV is now used
instead of DGEMM). One can now choose from alternative matrix product
implementations via options(matprod = ). The
"internal" implementation is not optimized for speed but
consistent in precision with other summations in R (using
long double accumulators where available).
"blas" calls BLAS directly for best speed, but usually with
undefined behavior for inputs with
NaN/Inf.
NEW FEATURES
User errors such as integrate(f, 0:1, 2) are now
caught.
Add signature argument to debug(),
debugonce(), undebug() and
isdebugged() for more conveniently debugging S3 and S4
methods. (Based on a patch by Gabe Becker.)
Add utils::debugcall() and
utils::undebugcall() for debugging the function that would
be called by evaluating the given expression. When the call is to an S4
generic or standard S3 generic, debugcall() debugs the
method that would be dispatched. A number of internal utilities were
added to support this, most notably
utils::isS3stdGeneric(). (Based on a patch by Gabe
Becker.)
Add utils::strcapture(). Given a character vector
and a regular expression containing capture expressions,
strcapture() will extract the captured tokens into a
tabular data structure, typically a data.frame.
str() and strOptions() get a new option
drop.deparse.attr with improved but changed
default behaviour for expressions. For expression objects
x, str(x) now may remove extraneous white
space and truncate long lines.
str(<looooooooong_string>) is no longer very
slow; inspired by Mikko Korpela’s proposal in .
str(x)’s default method is more “accurate” and hence
somewhat more generous in displaying character vectors; this will
occasionally change R outputs (and need changes to some
*.Rout(.save) files).
For a classed integer vector such as
x <- xtabs(~ c(1,9,9,9)), str(x) now shows
both the class and "int", instead of only the
latter.
isSymmetric(m) is much faster for large asymmetric
matrices m via pre-tests and a new option
tol1 (with which strict back compatibility is possible but
not the default).
The result of eigen() now is of class
"eigen" in the default case when eigenvectors are
computed.
Zero-length date and date-time objects (of classes
"POSIX[cl]?t") now print()
“recognizably”.
xy.coords() and xyz.coords() get a new
setLab option.
The method argument of sort.list(),
order() and sort.int() gains an
"auto" option (the default) which should behave the same as
before when method was not supplied.
stopifnot(E, ..) now reports differences when
E is a call to all.equal() and that is not
true.
boxplot(<formula>, *) gain optional arguments
drop, sep, and lex.order to pass
to split.default() which itself gains an argument
lex.order to pass to interaction() for more
flexibility.
The plot() method for ppr() has
enhanced default labels (xmin and
main).
sample.int() gains an explicit useHash
option (with a back compatible default).
identical() gains an ignore.srcref
option which drops "srcref" and similar attributes when
true (as by default).
diag(x, nrow = n) now preserves
typeof(x), also for logical, integer and raw x
(and as previously for complex and numeric).
smooth.spline() now allows direct specification of
lambda, gets a hatvalues() method and keeps
tol in the result, and optionally parts of the internal
matrix computations.
addNA() is faster now, e.g. when applied twice.
(Part of .)
New option rstandard(<lm>, type = "predicted")
provides the “PRESS”–related leave-one-out cross-validation errors for
linear models.
After seven years of deprecation, duplicated factor levels now
produce a warning when printed and an error in levels<-
instead of a warning.
Invalid factors, e.g., with duplicated levels (invalid but
constructable) now give a warning when printed, via new
function .valid.factor().
sessionInfo() has been updated for Apple’s change in
OS naming as from ‘10.12’ (‘macOS Sierra’ vs ‘OS X El
Capitan’). Its toLatex() method now includes the
running component.
options(interrupt=) can be used to specify a default
action for user interrupts. For now, if this option is not set and the
error option is set, then an unhandled user interrupt
invokes the error option. (This may be dropped in the
future as interrupt conditions are not error
conditions.)
In most cases user interrupt handlers will be called with a
"resume" restart available. Handlers can invoke this
restart to resume computation. At the browser prompt the r
command will invoke a "resume" restart if one is available.
Some read operations cannot be resumed properly when interrupted and do
not provide a "resume" restart.
Radix sort is now chosen by method = "auto" for
sort.int() for double vectors (and hence used for
sort() for unclassed double vectors), excluding ‘long’
vectors. sort.int(method = "radix") no longer rounds double
vectors.
The default and data.frame methods for
stack() preserve the names of empty elements in the levels
of the ind column of the return value. Set the new
drop argument to TRUE for the previous
behavior.
Speedup in simplify2array() and hence
sapply() and mapply() (for the case of names
and common length > 1), thanks to Suharto Anggono’s .
table(x, exclude = NULL) now sets
useNA = "ifany" (instead of "always").
Together with the bug fixes for this case, this recovers more consistent
behaviour compatible to older versions of R. As a consequence,
summary() for a logical vector no longer reports (zero)
counts for NA when there are no NAs.
dump.frames() gets a new option
include.GlobalEnv which allows to also dump the global
environment, thanks to Andreas Kersting’s proposal in .
system.time() now uses message()
instead of cat() when terminated early, such that
suppressMessages() has an effect; suggested by Ben
Bolker.
citation() supports inst/CITATION files
from package source trees, with lib.loc pointing to the
directory containing the package.
try() gains a new argument outFile with
a default that can be modified via
options(try.outFile = .), useful notably for
Sweave.
The unexported low-level functions in package parallel
for passing serialized R objects to and from forked children now support
long vectors on 64-bit platforms. This removes some limits on
higher-level functions such as mclapply() (but returning
gigabyte results from forked processes via serialization should
be avoided if at all possible).
Connections now print() without error even if
invalid, e.g. after having been destroyed.
apropos() and
find(simple.words = FALSE) no longer match object names
starting with . which are known to be internal objects
(such as .__S3MethodsTable__.).
Convenience function hasName() has been added; it is
intended to replace the common idiom !is.null(x$name)
without the usually unintended partial name matching.
strcapture() no longer fixes column names nor
coerces strings to factors (suggested by Bill Dunlap).
strcapture() returns NA for
non-matching values in x (suggested by Bill
Dunlap).
source() gets new optional arguments, notably
exprs; this is made use of in the new utility function
withAutoprint().
sys.source() gets a new toplevel.env
argument. This argument is useful for frameworks running package tests;
contributed by Tomas Kalibera.
Sys.setFileTime() and
file.copy(copy.date = TRUE) will set timestamps with
fractions of seconds on platforms/filesystems which support
this.
(Windows only.) file.info() now returns file
timestamps including fractions of seconds; it has done so on other
platforms since R 2.14.0. (NB: some filesystems do not record
modification and access timestamps to sub-second resolution.)
The license check enabled by
options(checkPackageLicense = TRUE) is now done when the
package’s namespace is first loaded.
ppr() and supsmu() get an optional
trace argument, and
ppr(.., sm.method = ..spline) is no longer limited to
sample size .
The POSIXct method for print() gets
optional tz and usetz arguments, thanks to a
report from Jennifer S. Lyon.
New function check_packages_in_dir_details() in
package tools for analyzing package-check log files to obtain
check details.
Package tools now exports function
CRAN_package_db() for obtaining information about current
packages in the CRAN package repository, and several functions for
obtaining the check status of these packages.
The (default) Stangle driver Rtangle allows
annotate to be a function and gets a new
drop.evalFALSE option.
The default method for quantile(x, prob) should now
be monotone in prob, even in border cases, see .
bug.report() now tries to extract an email address
from a BugReports field, and if there is none, from a
Contacts field.
The format() and print() methods for
object.size() results get new options standard
and digits; notably, standard = "IEC" and
standard = "SI" allow more standard (but less common)
abbreviations than the default ones, e.g. for kilobytes. (From
contributions by Henrik Bengtsson.)
If a reference class has a validity method,
validObject will be called automatically from the default
initialization method for reference classes.
tapply() gets new option default = NA
allowing to change the previously hardcoded value.
read.dcf() now consistently interprets any
‘whitespace’ to be stripped to include newlines.
The maximum number of DLLs that can be loaded into R
e.g. via dyn.load() can now be increased by
setting the environment variable R_MAX_NUM_DLLS before
starting R.
Assigning to an element of a vector beyond the current length now
over-allocates by a small fraction. The new vector is marked internally
as growable, and the true length of the new vector is stored in the
truelength field. This makes building up a vector result by
assigning to the next element beyond the current length more efficient,
though pre-allocating is still preferred. The implementation is subject
to change and not intended to be used in packages at this time.
Loading the parallel package namespace no longer sets or
changes the .Random.seed, even if
R_PARALLEL_PORT is unset. NB: This can break
reproducibility of output, and did for a CRAN package.
Methods "wget" and "curl" for
download.file() now give an R error rather than a non-zero
return value when the external command has a non-zero status.
Encoding name "utf8" is mapped to
"UTF-8". Many implementations of iconv accept
"utf8", but not GNU libiconv (including the late
2016 version 1.15).
sessionInfo() shows the full paths to the library or
executable files providing the BLAS/LAPACK implementations currently in
use (not available on Windows).
The binning algorithm used by bandwidth selectors
bw.ucv(), bw.bcv() and bw.SJ()
switches to a version linear in the input size n for
n > nb/2. (The calculations are the same, but for larger
n/nb it is worth doing the binning in advance.)
There is a new option PCRE_study which controls when
grep(perl = TRUE) and friends ‘study’ the compiled pattern.
Previously this was done for 11 or more input strings: it now defaults
to 10 or more (but most examples need many more for the difference from
studying to be noticeable).
grep(perl = TRUE) and friends can now make use of
PCRE’s Just-In-Time mechanism, for PCRE 8.20 on platforms where JIT is
supported. It is used by default whenever the pattern is
studied (see the previous item). (Based on a patch from Mikko Korpela.)
This is controlled by a new option PCRE_use_JIT.
Note that in general this makes little difference to the speed, and may take a little longer: its benefits are most evident on strings of thousands of characters. As a side effect it reduces the chances of C stack overflow in the PCRE library on very long strings (millions of characters, but see next item).
Warning: segfaults were seen using PCRE with JIT enabled on 64-bit Sparc builds.
There is a new option PCRE_limit_recursion for
grep(perl = TRUE) and friends to set a recursion limit
taking into account R’s estimate of the remaining C stack space (or
10000 if that is not available). This reduces the chance of C stack
overflow, but because it is conservative may report a non-match (with a
warning) in examples that matched before. By default it is enabled if
any input string has 1000 or more bytes. ()
getGraphicsEvent() now works on
X11(type = "cairo") devices. Thanks to Frederick Eaton (for
reviving an earlier patch).
There is a new argument onIdle for
getGraphicsEvent(), which allows an R function to be run
whenever there are no pending graphics events. This is currently only
supported on X11 devices. Thanks to Frederick Eaton.
The deriv() and similar functions now can compute
derivatives of log1p(), sinpi() and similar
one-argument functions, thanks to a contribution by Jerry
Lewis.
median() gains a formal ... argument,
so methods with extra arguments can be provided.
strwrap() reduces indent if it is more
than half width rather than giving an error. (Suggested by
Bill Dunlap.)
When the condition code in if(.) or
while(.) is not of length one, an error instead of a
warning may be triggered by setting an environment variable, see the
help page.
Formatting and printing of bibliography entries
(bibentry) is more flexible and better documented. Apart
from setting options(citation.bibtex.max = 99) you can also
use print(<citation>, bibtex=TRUE) (or
format(..)) to get the BibTeX entries in the case of more
than one entry. This also affects citation(). Contributions
to enable style = "html+bibtex" are welcome.
C-LEVEL FACILITIES
Entry points R_MakeExternalPtrFn and
R_ExternalPtrFn are now declared in header
Rinternals.h to facilitate creating and retrieving an R
external pointer from a C function pointer without ISO C warnings about
the conversion of function pointers.
There was an exception for the native Solaris C++ compiler to the
dropping (in R 3.3.0) of legacy C++ headers from headers such as
R.h and Rmath.h — this has now been removed.
That compiler has strict C++98 compliance hence does not include
extensions in its (non-legacy) C++ headers: some packages will need to
request C++11 or replace non-C++98 calls such as lgamma:
see §1.6.4 of ‘Writing R Extensions’. Because it is needed by about 70
CRAN packages, headers R.h and Rmath.h still
declare
std;
when included on Solaris.
When included from C++, the R headers now use forms such as
std::FILE directly rather than including the line
std::FILE;
C++ code including these headers might be relying on the latter.
Headers R_ext/BLAS.h and R_ext/Lapack.h
have many improved declarations including const for
double-precision complex routines. Inter alia this avoids
warnings when passing ‘string literal’ arguments from C++11
code.
Headers for Unix-only facilities
R_ext/GetX11Image.h, R_ext/QuartzDevice.h and
R_ext/eventloop.h are no longer installed on
Windows.
No-longer-installed headers GraphicsBase.h,
RGraphics.h, Rmodules/RX11.h and
Rmodules/Rlapack.h which had a LGPL license no longer do
so.
HAVE_UINTPTR_T is now defined where appropriate by
Rconfig.h so that it can be included before
Rinterface.h when CSTACK_DEFNS is defined and
a C compiler (not C++) is in use. Rinterface.h now includes
C header stdint.h or C++11 header cstdint
where needed.
Package tools has a new function
package_native_routine_registration_skeleton() to assist
adding native-symbol registration to a package. See its help and §5.4.1
of ‘Writing R Extensions’ for how to use it. (At the time it was added
it successfully automated adding registration to over 90% of CRAN
packages which lacked it. Many of the failures were newly-detected bugs
in the packages, e.g. 50 packages called entry points with varying
numbers of arguments and 65 packages called entry points not in the
package.)
INSTALLATION on a UNIX-ALIKE
readline headers (and not just the library) are
required unless configuring with –with-readline=no.configure now adds a compiler switch for C++11 code,
even if the compiler supports C++11 by default. (This ensures that
g++ 6.x uses C++11 mode and not its default mode of C++14
with ‘GNU extensions’.) The tests for C++11 compliance are now much more
comprehensive. For gcc < 4.8, the tests from R 3.3.0 are used in
order to maintain the same behaviour on Linux distributions with
long-term support.CXX11, not CXX1X. Likewise C++11 flags are
specified with CXX11FLAGS and the standard (e.g.,
-std=gnu++11) is specified with CXX11STD.configure now tests for a C++14-compliant compiler by
testing some basic features. This by default tries flags for the
compiler specified by CXX11, but an alternative compiler,
options and standard can be specified by variables CXX14,
CXX14FLAGS and CXX14STD (e.g.,
-std=gnu++14).CXXSTD to help specify the
standard for C++ code, e.g. -std=c++98. This makes it
easier to work with compilers which default to a later standard: for
example, with CXX=g++6 CXXSTD=-std=c++98
configure will select commands for g++ 6.x
which conform to C++11 and C++14 where specified but otherwise use
C++98.configure checks that the compiler specified by
$CXX $CXXFLAGS is able to compile C++ code.configure checks for the required header
sys/select.h (or sys/time.h on legacy systems)
and system call select and aborts if they are not
found.utimensat will
be used by Sys.setFileTime() and
file.copy(copy.date = TRUE). This may result in slightly
more accurate file times. (It is available on Linux and FreeBSD but not
macOS.)libcurl has been
reduced to 7.22.0, although at least 7.28.0 is preferred and earlier
versions are little tested. (This is to support Debian 7 ‘Wheezy’ LTS
and Ubuntu ‘Precise’ 12.04 LTS, although the latter is close to
end-of-life.)configure tests for a C++17-compliant compiler. The
tests are experimental and subject to change in the future.INCLUDED SOFTWARE
tcltk*.chm help file is no longer included;
please consult the online help at http://www.tcl.tk/man/ instead.PACKAGE INSTALLATION
LinkingTo other packages has
been changed so their include directories come earlier, before those
specified in CPPFLAGS. This will only have an effect if
non-system include directories are included with -I flags
in CPPFLAGS (and so not the default
-I/usr/local/include which is treated as a system include
directory on most platforms)..C or
.Fortran need to be re-installed for this version (unless
installed with R-devel SVN revision r72375 or later).CXX1X are
deprecated in favour of those using CXX11, but for the time
being are still made available via file
etc/Makeconf. Packages using them should be converted to
the new forms and made dependent on R (>= 3.4.0).UTILITIES
R CMD check –as-cran with
_R_CHECK_CRAN_INCOMING_REMOTE_ false now skips tests that
require remote access. The remaining (local) tests typically run quickly
compared to the remote tests.R CMD build will now give priority to vignettes
produced from files in the vignettes directory over those
in the inst/doc directory, with a warning that the latter
are being ignored.R CMD config gains a –all option for
printing names and values of all basic configure variables. It now knows
about all the variables used for the C++98, C++11 and C++14
standards.R CMD check now checks that output files in
inst/doc are newer than the source files in
vignettes.*.r in the tests directory are now recognized
as tests by R CMD check. (Wish of .)R CMD build and R CMD check now use the
union of R_LIBS and .libPaths(). They
may not be equivalent, e.g., when the latter is determined by
R_PROFILE.R CMD build now preserves dates when it copies files in
preparing the tarball. (Previously on Windows it changed the dates on
all files; on Unix, it changed some dates when installing
vignettes.)R CMD check –no-stop-on-test-error
allows running the remaining tests (under tests/) even if
one gave an error..Call() and .External() calls
which alter their arguments is described in §8 of the ‘R Internals’
manual.R CMD check now checks any BugReports
field to be non-empty and a suitable single URL.R CMD check –as-cran now NOTEs if the package does not
register its native routines or does not declare its intentions on
(native) symbol search. (This will become a WARNING in due course.)DEPRECATED AND DEFUNCT
setInternet2() is defunct.readline emulations based on
editline (aka libedit) is deprecated.NO_C_HEADERS is defunct and
silently ignored.unix.time(), a traditional synonym for
system.time(), has been deprecated.structure(NULL, ..) is now deprecated as you cannot set
attributes on .Rconfig.h no longer defines
SUPPORT_OPENMP; instead use _OPENMP (as
documented for a long time).styles member of the R_CMethodDef and
R_FortranMethodDef structures has been removed. Packages
using these will need to be re-installed for R 3.4.0.BUG FIXES
Getting or setting body() or formals()
on non-functions for now signals a warning and may become an error for
setting.
match(x, t), duplicated(x) and
unique(x) work as documented for complex numbers with
NAs or NaNs, where all those containing
NA do match, whereas in the case of NaN’s both
real and imaginary parts must match, compatibly with how
print() and format() work for complex
numbers.
deparse(<complex>, options = "digits17")
prints more nicely now, mostly thanks to a suggestion by Richie
Cotton.
Rotated symbols in plotmath expressions are now positioned
correctly on x11(type = "Xlib"). ()
as<-() avoids an infinite loop when a virtual
class is interposed between a subclass and an actual
superclass.
Fix level propagation in unlist() when the list
contains zero-length lists or factors.
Fix S3 dispatch on S4 objects when the methods package is not attached.
Internal S4 dispatch sets .Generic in the method
frame for consistency with standardGeneric(). ()
Fix order(x, decreasing = TRUE) when x
is an integer vector containing MAX_INT. Ported from a fix
Matt Dowle made to .
Fix caching by callNextMethod(), resolves and
.
grouping() puts NAs last, to be consistent with the
default behavior of order().
Point mass limit cases: qpois(-2, 0) now gives
NaN with a warning and qgeom(1, 1) is
0. ()
table() no longer drops an "NaN" factor
level, and better obeys exclude = <chr>, thanks to
Suharto Anggono’s patch for . Also, in the case of
exclude = NULL and NAs, these are tabulated
correctly (again). Further,
table(1:2, exclude = 1, useNA = "ifany") no longer
erroneously reports <NA> counts.
Additionally, all cases of empty exclude are equivalent,
and useNA is not overwritten when specified (as it was by
exclude = NULL).
wilcox.test(x, conf.int=TRUE) no longer errors out
in cases where the confidence interval is not available, such as for
x = 0:2.
droplevels(f) now keeps <NA> levels when
present.
In integer arithmetic, NULL is now treated as
integer(0) whereas it was previously treated as
double(0).
The radix sort considers NA_real_ and
NaN to be equivalent in rank (like the other sort
algorithms).
When index.return=TRUE is passed to
sort.int(), the radix sort treats NAs like
sort.list() does (like the other sort algorithms).
When in tabulate(bin, nbin) length(bin)
is larger than the maximal integer, the result is now of type
double and hence no longer silently overflows to wrong
values. ()
as.character.factor() respects S4 inheritance when
checking the type of its argument. ()
The factor method for print() no longer
sets the class of the factor to NULL, which would violate a
basic constraint of an S4 object.
formatC(x, flag = f) allows two new flags, and
signals an error for invalid flags also in the case of character
formatting.
Reading from file("stdin") now also closes the
connection and hence no longer leaks memory when reading from a full
pipe, thanks to Gábor Csárdi, see thread starting at https://stat.ethz.ch/pipermail/r-devel/2016-November/073360.html.
Failure to create file in tempdir() for compressed
pdf() graphics device no longer errors (then later
segfaults). There is now a warning instead of error and compression is
turned off for the device. Thanks to Alec Wysoker ().
Asking for methods() on "|" returns
only S3 methods. See https://stat.ethz.ch/pipermail/r-devel/2016-December/073476.html.
dev.capture() using Quartz Cocoa device (macOS)
returned invalid components if the back-end chose to use ARGB instead of
RGBA image format. (Reported by Noam Ross.)
seq("2", "5") now works too, equivalently to
"2":"5" and seq.int().
seq.int(to = 1, by = 1) is now correct, other cases
are integer (instead of double) when seq() is
integer too, and the "non-finite" error messages are consistent between
seq.default() and seq.int(), no longer
mentioning NaN etc.
rep(x, times) and rep.int(x, times) now
work when times is larger than the largest value
representable in an integer vector. ()
download.file(method = "libcurl") does not check for
URL existence before attempting downloads; this is more robust to
servers that do not support HEAD or range-based retrieval, but may
create empty or incomplete files for aborted download requests.
Bandwidth selectors bw.ucv(), bw.bcv()
and bw.SJ() now avoid integer overflow for large sample
sizes.
str() no longer shows
"list output truncated", in cases that list was not shown
at all. Thanks to Neal Fultz ()
Fix for cairo_pdf() (and svg() and
cairo_ps()) when replaying a saved display list that
contains a mix of grid and graphics output. (Report by
Yihui Xie.)
The str() and as.hclust() methods for
"dendrogram" now also work for deeply nested dendrograms
thanks to non-recursive implementations by Bradley Broom.
sample() now uses two uniforms for added precision
when the uniform generator is Knuth-TAOCP,
Knuth-TAOCP-2002, or a user-defined generator and the
population size is or greater.
If a vignette in the vignettes directory is listed
in .Rbuildignore, R CMD build would not
include it in the tarball, but would include it in the vignette
database, leading to a check warning. ()
tools::latexToUtf8() infinite looped on certain
inputs. ()
terms.formula() ignored argument names when
determining whether two terms were identical. ()
callNextMethod() was broken when called from a
method that augments the formal arguments of a primitive
generic.
Coercion of an S4 object to a vector during sub-assignment into a
vector failed to dispatch through the as.vector() generic
(often leading to a segfault).
Fix problems in command completion: Crash () and junk display in Windows, handling special characters in filenames on all systems.
CHANGES IN R 3.3.3
NEW FEATURES
http:// URL to a
https:// URL is encountered:
download.file() and
url() now report that they cannot follow this (rather than
failing silently).download.file(method = "auto") (the
default) re-tries with method = "libcurl".url(method = "default") with an explicit
open argument re-tries with
method = "libcurl". This covers many of the usages,
e.g. readLines() with a URL argument.INSTALLATION on a UNIX-ALIKE
configure check for the zlib version
is now robust to versions longer than 5 characters, including
1.2.11.UTILITIES
_R_CHECK_TESTS_NLINES_ controls
how R CMD check reports failing tests (see §8 of the ‘R
Internals’ manual).DEPRECATED AND DEFUNCT
styles field of the components of R_CMethodDef
and R_FortranMethodDef is deprecated.BUG FIXES
vapply(x, *) now works with long vectors
x. ()isS3method("is.na.data.frame") and similar are correct
now. ()grepRaw(<long>, <short>, fixed = TRUE) now
works, thanks to a patch by Mikko Korpela. ()Sys.readlink() works, resolving ."Cincinnati" was missing an "n" in the
precip dataset.pdf() when loading
an encoding file. Reported by Talos (TALOS-2016-0227).getDLLRegisteredRoutines() now produces its warning
correctly when multiple DLLs match, thanks to Matt Dowle’s .Sys.timezone() now returns non-NA also on platforms
such as Ubuntu 14.04.5 LTS, thanks to Mikko Korpela’s
.format(x) for an illegal "POSIXlt" object
x no longer segfaults.methods(f) now also works for f
"(" or "{".dir.create() did not check the length of
the path to create, and so could overflow a buffer and crash R. ()pmin() and pmax() now work again for
ordered factors and 0-length S3 classed objects, thanks to
Suharto Anggono’s and .bug.report() did not do any validity checking on a
package’s BugReports field. It now ignores an empty field,
removes leading whitespace and only attempts to open
http:// and https:// URLs, falling back to
emailing the maintainer.bw.ucv() and bw.SJ()
gave incorrect answers or incorrectly reported an error (because of
integer overflow) for inputs longer than 46341. Similarly for
bw.bcv() at length 5793. Another possible integer overflow
is checked and may result in an error report (rather than an incorrect
result) for much longer inputs (millions for a smooth
distribution).findMethod() failed if the active signature had
expanded beyond what a particular package used. (Example with packages
and on CRAN.)qbeta() underflowed too early in some very asymmetric
cases. ()R CMD Rd2pdf had problems with packages with non-ASCII
titles in .Rd files (usually the titles were omitted).CHANGES IN R 3.3.2
NEW FEATURES
extSoftVersion() now reports the version (if any) of
the readline library in use.eigen().options(deparse.max.lines=) to limit the number of
lines recorded in .Traceback and other deparsing
activities.format(<AsIs>) looks more regular, also for
non-character atomic matrices.abbreviate() gains an option
named = TRUE.setMethod() no longer print a message when
creating a generic function in those cases where that is natural: S3
generics and primitives.INSTALLATION and INCLUDED SOFTWARE
readline library >= 6.3 had been
changed so that terminal window resizes were not signalled to
readline: code has been added using a explicit signal
handler to work around that (when R is compiled against readline >=
6.3). ()configure works better with Oracle Developer Studio
12.5.UTILITIES
R CMD check reports more dubious flags in files
src/Makevars[.in], including -w and
-g.R CMD check has been set up to filter important
warnings from recent versions of gfortran with
-Wall -pedantic: this now reports non-portable GNU
extensions such as out-of-order declarations.R CMD config works better with paths containing spaces,
even those of home directories (as reported by Ken Beath).DEPRECATED AND DEFUNCT
NO_C_HEADERS is deprecated (no C
headers are included by R headers from C++ as from R 3.3.0, so it should
no longer be needed).BUG FIXES
R CMD check could
be stymied by src/Makevars files which contained
targets.Rterm to stop accepting input. (; patch
submitted by Jan Gleixner.)pretty(d, ..) behaves better for date-time
d ().ClassExtends object
when looking up superclasses in the cache.sample(NA_real_) now works.merge(df1, df2) now also works for data frames with
column names "na.last", "decreasing", or
"method". ()contour() caused a segfault if the labels
argument had length zero. (Reported by Bill Dunlap.)unique(warnings()) works more correctly, thanks to a
new duplicated.warnings() method.findInterval(x, vec = numeric(), all.inside = TRUE) now
returns 0s as documented. (Reported by Bill Dunlap.)R CMD SHLIB failed when a symbol in the
resulting library had the same name as a keyword in the
.def file. ()pmax() and pmin() now work with (more ?)
classed objects, such as "Matrix" from the package, as
documented for a long time.axis(side, x = D) and hence Axis() and
plot() now work correctly for "Date" and time
objects D, even when “time goes backward”, e.g., with
decreasing xlim. (Reported by William May.)str(I(matrix(..))) now looks as always intended.plot.ts(), the plot() method for time
series, now respects cex, lwd and
lty. (Reported by Greg Werbin.)parallel::mccollect() now returns a named list (as
documented) when called with wait = FALSE. (Reported by
Michel Lang.)c()’s argument use.names is documented
now, as belonging to the (C internal) default method. In “parallel”,
argument recursive is also moved from the generic to the
default method, such that the formal argument list of base
generic c() is just (...).rbeta(4, NA) and similarly rgamma() and
rnbinom() now return NaN’s with a warning, as
other r<dist>(), and as documented. ()options(checkPackageLicense = TRUE) no longer
requires acceptance of the licence for non-default standard packages
such as compiler. (Reported by Mikko Korpela.)split(<very_long>, *) now works even when the
split off parts are long. ()min() and max() now also work correctly
when the argument list starts with character(0). ()prod(dim(.)) >= 2^31) now works thanks to Michael
Schubmehl’s .bartlett.test() used residual sums of squares instead
of variances, when the argument was a list of lm objects.
(Reported by Jens Ledet Jensen).plot(<lm>, which = *) now correctly labels the
contour lines for the standardized residuals for which = 6.
It also takes the correct in case of singularities (also for
which = 5). ()xtabs(~ exclude) no longer fails from wrong scope,
thanks to Suharto Anggono’s .methods() did not re-analyse
previously defined methods, meaning that calls to methods defined later
would fail. (Reported by Charles Tilford).findInterval(x, vec, left.open = TRUE) misbehaved in
some cases. (Reported by Dmitriy Chernykh.)CHANGES IN R 3.3.1
BUG FIXES
R CMD INSTALL and hence install.packages()
gave an internal error installing a package called description
from a tarball on a case-insensitive file system.match(x, t) (and hence x %in% t) failed
when x was of length one, and either character
and x and t only differed in their
Encoding or when x and t where
complex with NAs or NaNs.
(.)unloadNamespace(ns) also works again when
ns is a ‘namespace’, as from
getNamespace().rgamma(1, Inf) or rgamma(1, 0, 0) no
longer give NaN but the correct limit.length(baseenv()) is correct now.pretty(d, ..) for date-time d rarely
failed when "halfmonth" time steps were tried () and on
‘inaccurate’ platforms such as 32-bit Windows or a configuration with
–disable-long-double; see comment #15 of .text.default(x, y, labels), the rarely(?) used
default for labels is now correct also for the case of a
2-column matrix x and missing y.as.factor(c(a = 1L)) preserves names()
again as in R < 3.1.0.strtrim(""[0], 0[0]) now works.Ctrl-C to terminate a reverse incremental search
started by Ctrl-R in the readline-based Unix
terminal interface is now supported when R was compiled against
readline >= 6.0 (Ctrl-G always worked).
()diff(<difftime>) now keeps the
"units" attribute, as subtraction already did, .CHANGES IN R 3.3.0
SIGNIFICANT USER-VISIBLE CHANGES
nchar(x, *)’s argument keepNA governing
how the result for NAs in x is determined,
gets a new default keepNA = NA which returns
NA where x is NA, except for
type = "width" which still returns 2, the
formatting / printing width of NA.https: URLs in the default
methods for download.file(), url() and code
making use of them. Unfortunately that cannot guarantee that any
particular https: URL can be accessed. For example, server
and client have to successfully negotiate a cryptographic protocol
(TLS/SSL, …) and the server’s identity has to be verifiable via
the available certificates. Different access methods may allow different
protocols or use private certificate bundles: we encountered a
https: CRAN mirror which could be accessed by one browser
but not by another nor by download.file() on the same Linux
machine.NEW FEATURES
The print method for methods() gains a
byclass argument.
New functions validEnc() and
validUTF8() to give access to the validity checks for
inputs used by grep() and friends.
Experimental new functionality for S3 method checking, notably
isS3method(). Also, the names of the R ‘language elements’
are exported as character vector tools::langElts.
str(x) now displays "Time-Series" also
for matrix (multivariate) time-series, i.e. when is.ts(x)
is true.
(Windows only) The GUI menu item to install local packages now
accepts *.tar.gz files as well as *.zip files
(but defaults to the latter).
New programmeR’s utility function
chkDots().
D() now signals an error when given invalid input,
rather than silently returning NA. (Request of John
Nash.)
formula objects are slightly more “first class”:
e.g., formula() or new("formula", y ~ x) are
now valid. Similarly, for "table", "ordered"
and "summary.table". Packages defining S4 classes with the
above S3/S4 classes as slots should be reinstalled.
New function strrep() for repeating the elements of
a character vector.
rapply() preserves attributes on the list when
how = "replace".
New S3 generic function sigma() with methods for
extracting the estimated standard deviation aka “residual standard
deviation” from a fitted model.
news() now displays R and package news files within
the HTML help system if it is available. If no news file is found, a
visible NULL is returned to the console.
as.raster(x) now also accepts raw
arrays x assuming values in 0:255.
Subscripting of matrix/array objects of type
"expression" is now supported.
type.convert("i") now returns a factor instead of a
complex value with zero real part and missing imaginary part.
Graphics devices cairo_pdf() and
cairo_ps() now allow non-default values of the
cairographics ‘fallback resolution’ to be set. This now defaults to 300
on all platforms: that is the default documented by cairographics, but
apparently was not used by all system installations.
file() gains an explicit method
argument rather than implicitly using
getOption("url.method", "default").
Thanks to a patch from Tomas Kalibera, x[x != 0] is
now typically faster than x[which(x != 0)] (in the case
where x has no NAs, the two are equivalent).
read.table() now always uses the names for a named
colClasses argument (previously names were only used when
colClasses was too short). (In part, wish of .)
(Windows only) download.file() with default
method = "auto" and a ftps:// URL chooses
"libcurl" if that is available.
The out-of-the box Bioconductor mirror has been changed to one
using https://: use chooseBioCmirror() to
choose a http:// mirror if required.
The data frame and formula methods for aggregate()
gain a drop argument.
available.packages() gains a repos
argument.
The undocumented switching of methods for url() on
https: and ftps: URLs is confined to
method = "default" (and documented).
smoothScatter() gains a ret.selection
argument.
qr() no longer has a ... argument to
pass additional arguments to methods.
[ has a method for class
"table".
It is now possible (again) to replayPlot() a display
list snapshot that was created by recordPlot() in a
different R session. It is still not a good idea to use snapshots as a
persistent storage format for R plots, but it is now not completely
silly to use a snapshot as a format for transferring an R plot between
two R sessions.
The underlying changes mean that packages providing graphics devices (e.g., , , , ) will need to be reinstalled.
Code for restoring snapshots was contributed by Jeroen Ooms and JJ Allaire.
Some testing code is available at https://github.com/pmur002/R-display-list.
tools::undoc(dir = D) and
codoc(dir = D) now also work when D is a
directory whose normalizePath()ed version does not end in
the package name, e.g. from a symlink.
abbreviate() has more support for multi-byte
character sets – it no longer removes bytes within characters and knows
about Latin vowels with accents. It is still only really suitable for
(most) European languages, and still warns on non-ASCII input.
abbreviate(use.classes = FALSE) is now implemented, and
that is more suitable for non-European languages.
match(x, table) is faster (sometimes by an order of
magnitude) when x is of length one and
incomparables is unchanged, thanks to Peter Haverty
().
More consistent, partly not back-compatible behavior of
NA and NaN coercion to complex numbers,
operations less often resulting in complex NA
(NA_complex_).
lengths() considers methods for length
and [[ on x, so it should work automatically
on any objects for which appropriate methods on those generics are
defined.
The logic for selecting the default screen device on OS X has
been simplified: it is now quartz() if that is available
even if environment variable DISPLAY has been set by the
user. The choice can easily be overridden via environment
variable R_INTERACTIVE_DEVICE.
On Unix-like platforms which support the getline C
library function, system(*, intern = TRUE) no longer
truncates (output) lines longer than 8192 characters, thanks to Karl
Millar. ()
rank() gains a ties.method = "last"
option, for convenience (and symmetry).
regmatches(invert = NA) can now be used to extract
both non-matched and matched substrings.
data.frame() gains argument
fix.empty.names; as.data.frame.list() gets new
cut.names, col.names and
fix.empty.names.
plot(x ~ x, *) now warns that it is the same as
plot(x ~ 1, *).
recordPlot() has new arguments load and
attach to allow package names to be stored as part of a
recorded plot. replayPlot() has new argument
reloadPkgs to load/attach any package names that were
stored as part of a recorded plot.
S4 dispatch works within calls to .Internal(). This
means explicit S4 generics are no longer needed for
unlist() and as.vector().
Only font family names starting with "Hershey" (and
not "Her" as before) are given special treatment by the
graphics engine.
S4 values are automatically coerced to vector (via
as.vector) when subassigned into atomic vectors.
findInterval() gets a left.open
option.
The version of LAPACK included in the sources has been updated to
3.6.0, including those ‘deprecated’ routines which were previously
included. Ca 40 double-complex routines have been added at the
request of a package maintainer. As before, the details of what is
included are in src/modules/lapack/README and this now
gives information on earlier additions.
tapply() has been made considerably more efficient
without changing functionality, thanks to proposals from Peter Haverty
and Suharto Anggono. ()
match.arg(arg) (the one-argument case) is faster; so
is sort.int(). ()
The format method for object_size
objects now also accepts “binary” units such as "KiB" and
e.g., "Tb". (Partly from .)
Profiling now records calls of the form foo::bar and
some similar cases directly rather than as calls to
<Anonymous>. Contributed by Winston Chang.
New string utilities startsWith(x, prefix) and
endsWith(x, suffix). Also provide speedups for some
grepl("^...", *) uses (related to proposals in ).
Reference class finalizers run at exit, as well as on garbage collection.
Avoid parallel dependency on stats for port choice and random number seeds. ()
The radix sort algorithm and implementation from
(forder) replaces the previous radix (counting) sort and
adds a new method for order(). Contributed by Matt Dowle
and Arun Srinivasan, the new algorithm supports logical, integer (even
with large values), real, and character vectors. It outperforms all
other methods, but there are some caveats (see
?sort).
The order() function gains a method
argument for choosing between "shell" and
"radix".
New function grouping() returns a permutation that
stably rearranges data so that identical values are adjacent. The return
value includes extra partitioning information on the groups. The
implementation came included with the new radix sort.
rhyper(nn, m, n, k) no longer returns
NA when one of the three parameters exceeds the maximal
integer.
switch() now warns when no alternatives are
provided.
parallel::detectCores() now has default
logical = TRUE on all platforms – as this was the default
on Windows, this change only affects Sparc Solaris. Option
logical = FALSE is now supported on Linux and recent
versions of OS X (for the latter, thanks to a suggestion of Kyaw
Sint).
hist() for "Date" or
"POSIXt" objects would sometimes give misleading labels on
the breaks, as they were set to the day before the start of the period
being displayed. The display format has been changed, and the shift of
the start day has been made conditional on right = TRUE
(the default). ()
R now uses a new version of the logo (donated to the R Foundation
by RStudio). It is defined in .svg format, so will resize
without unnecessary degradation when displayed on HTML pages—there is
also a vector PDF version. Thanks to Dirk Eddelbuettel for producing the
corresponding X11 icon.
New function .traceback() returns the stack trace
which traceback() prints.
lengths() dispatches internally.
dotchart() gains a pt.cex argument to
control the size of points separately from the size of plot labels.
Thanks to Michael Friendly and Milan Bouchet-Valat for ideas and
patches.
as.roman(ch) now correctly deals with more diverse
character vectors ch; also arithmetic with the resulting
roman numbers works in more cases. ()
prcomp() gains a new option rank.
allowing to directly aim for less than min(n,p) PC’s. The
summary() and its print() method have been
amended, notably for this case.
gzcon() gains a new option text, which
marks the connection as text-oriented (so e.g. pushBack()
works). It is still always opened in binary mode.
The import() namespace directive now accepts an
argument except which names symbols to exclude from the
imports. The except expression should evaluate to a
character vector (after substituting symbols for strings). See Writing R
Extensions.
New convenience function Rcmd() in package
tools for invoking R CMD tools from within
R.
New functions makevars_user() and
makevars_site() in package tools to determine the
location of the user and site specific Makevars files for
customizing package compilation.
UTILITIES
R CMD check has a new option
–ignore-vignettes for use with non-Sweave vignettes whose
VignetteBuilder package is not available.R CMD check now by default checks code usage
(via ) with only the base package attached. Functions from
default packages other than base which are used in the package
code but not imported are reported as undefined globals, with a
suggested addition to the NAMESPACE file.R CMD check –as-cran now also checks DOIs in package
CITATION and Rd files.R CMD Rdconv and R CMD Rd2pdf each have a
new option –RdMacros=pkglist which allows Rd macros to be
specified before processing.DEPRECATED AND DEFUNCT
zlib,
bzip2, xz and PCRE have been removed, so
suitable external (usually system) versions are required (see the ‘R
Installation and Administration’ manual).cairo_bmp(), cairo_png() and
cairo_tiff() have been removed. (These devices should be
used as e.g. bmp(type = "cairo").)setInternet2() has no effect
and will be removed in due course. The choice between methods
"internal" and "wininet" is now made by the
method arguments of url() and
download.file() and their defaults can be set via
options. The out-of-the-box default remains "wininet" (as
it has been since R 3.2.2).[<- with an S4 value into a list currently embeds
the S4 object into its own list such that the end result is roughly
equivalent to using [[<-. That behavior is deprecated.
In the future, the S4 value will be coerced to a list with
as.list().package.dependencies(), pkgDepends(), etc are
deprecated now, mostly in favor of package_dependencies()
which is both more flexible and efficient.INSTALLATION and INCLUDED SOFTWARE
valgrind (e.g., 3.3.0)
has been removed.libtool script (generated by
configure) has been updated to version 2.4.6 (from
2.2.6a).libcurl version 7.28.0 or later with support for the
https protocol is required for installation (except on
Windows).capabilities("http/ftp") is always true.configure uses pkg-config for PNG, TIFF
and JPEG where this is available. This should work better with multiple
installs and with those using static libraries.configure default on OS X is
–disable-R-framework: enable this if you intend to install
under /Library/Frameworks and use with
R.app.configure), but will still be accepted until
R 3.4.0.configure looks for C functions __cospi,
__sinpi and __tanpi and uses these if
cospi etc are not found. (OS X is the main
instance.)gcc 4.9.3. This build
will require recompilation of at least those packages that include C++
code, and possibly others. A build of R-devel using the older toolchain
will be temporarily available for comparison purposes. During the
transition, the environment variable R_COMPILED_BY has been
defined to indicate which toolchain was used to compile R (and hence,
which should be used to compile code in packages). The
COMPILED_BY variable described below will be a permanent
replacement for this.make and R CMD config variable
named COMPILED_BY has been added. This indicates which
toolchain was used to compile R (and hence, which should be used to
compile code in packages).PACKAGE INSTALLATION
make macro AWK which used to be made
available to files such as src/Makefile is no longer
set.C-LEVEL FACILITIES
The API call logspace_sum introduced in R 3.2.0 is
now remapped as an entry point to Rf_logspace_sum, and its
first argument has gained a const qualifier. () Code using
it will need to be reinstalled.
Similarly, entry point log1pexp also defined in
Rmath.h is remapped there to
Rf_log1pexp
R_GE_version has been increased to
11.
New API call R_orderVector1, a faster one-argument
version of R_orderVector.
When R headers such as R.h and Rmath.h
are called from C++ code in packages they include the C++ versions of
system headers such as <cmath> rather than the legacy
headers such as <math.h>. (Headers
Rinternals.h and Rinterface.h already did, and
inclusion of system headers can still be circumvented by defining
NO_C_HEADERS, including as from this version for those two
headers.) The manual has long said that R headers should be included
within an extern "C" block, and almost all the packages
affected by this change were doing so.
Including header S.h from C++ code would fail on
some platforms, and so gives a compilation error on all.
The deprecated header Rdefines.h is now compatible
with defining R_NO_REMAP.
The connections interface now includes a function
R_GetConnection() which allows packages implementing
connections to convert R connection objects to
Rconnection handles. Code which previously used the
low-level R-internal getConnection() entry point should
switch.
BUG FIXES
asChar(x) is fixed for when x is
not a vector, and it returns "TRUE"/"FALSE"
instead of "T"/"F" for logical vectors..colSums() etc (with an initial
dot) are now named x rather than X (matching
colSums()): thus error messages are corrected.coef() method for class "maov" has been
added to allow vcov() to work with multivariate results.
()method = "libcurl" connections signal errors rather
than retrieving HTTP error pages (where the ISP reports the error).xpdrows.data.frame() was not checking for unique row
names; in particular, this affected assignment to non-existing rows
via numerical indexing. ()tail.matrix() did not work for zero rows matrices, and
could produce row “labels” such as "[1e+05,]"."stringsAsFactors" now
format and print correctly. ()cor() is now guaranteed to return a value with absolute
value less than or equal to 1. ()names(dim(.)).data.frame method of rbind()
construction row.names works better in borderline integer
cases, but may change the names assigned. ()getGraphicsEvent() miscoded buttons and
missed mouse motion events. ()methods(round) now also lists
round.POSIXt.tar() now works with the default
files = NULL. ()on.exit() actions are
established instead of trying to run all on.exit() actions
before jumping to the final target. This unwinds the stack gradually,
releases resources held on the stack, and significantly reduces the
chance of a segfault when running out of C stack space. Error handlers
established using withCallingHandlers() and
options("error") specifications are ignored when handling a
C stack overflow error as attempting one of these would trigger a
cascade of C stack overflow errors. (These changes resolve .)pretty(d, n, min.n, *) for date-time objects
d works again in border cases with large
min.n, returns a labels attribute also for
small-range dates and in such cases its returned length is closer to the
desired n. () Additionally, it finally does cover the range
of d, as it always claimed.tsp(x) <- NULL did not handle correctly objects
inheriting from both "ts" and "mts". ()install.packages() could give false errors when
options("pkgType") was "binary". (Reported by
Jose Claudio Faria.)locator() in
X11, but introduced problems in Windows. Now both should be fixed.
()download.file() with method = "wininet"
incorrectly warned of download file length difference when reported
length was unknown. ()diag(NULL, 1) crashed because of missed type checking.
()CHANGES IN R 3.2.5
BUG FIXES
format.POSIXlt() behaved incorrectly in R 3.2.4.
E.g. the output of
format(as.POSIXlt(paste0(1940:2000, "-01-01"), tz = "CET"), usetz = TRUE)
ended in two "CEST" time formats.CHANGES IN R 3.2.4
NEW FEATURES
install.packages() and related functions now give a
more informative warning when an attempt is made to install a base
package.summary(x) now prints with less rounding when
x contains infinite values. (Request of .)provideDimnames() gets an optional unique
argument.shQuote() gains type = "cmd2" for quoting
in cmd.exe in Windows. (Response to .)data.frame method of rbind() gains an
optional argument stringsAsFactors (instead of only
depending on getOption("stringsAsFactors")).smooth(x, *) now also works for long vectors.tools::texi2dvi() has a workaround for problems with
the texi2dvi script supplied by texinfo 6.1. It
extracts more error messages from the LaTeX logs when in emulation
mode.UTILITIES
R CMD check will leave a log file
build_vignettes.log from the re-building of vignettes in
the .Rcheck directory if there is a problem, and always if
environment variable _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_
is set to a true value.DEPRECATED AND DEFUNCT
SUPPORT_OPENMP from header
Rconfig.h is deprecated in favour of the standard OpenMP
define _OPENMP. (This has been the recommendation in the
manual for a while now.)make macro AWK which is long unused by
R itself but recorded in file etc/Makeconf is deprecated
and will be removed in R 3.3.0.S.h is no longer documented: its use
should be replaced by R.h.BUG FIXES
kmeans(x, centers = <1-row>) now works. ()Vectorize() now checks for clashes in argument names.
()file.copy(overwrite = FALSE) would signal a successful
copy when none had taken place. ()ngettext() now uses the same default domain as
gettext(). ()array(.., dimnames = *) now warns about
non-list dimnames and, from R 3.3.0, will signal the same
error for invalid dimnames as matrix() has always
done.addmargins() now adds dimnames for the extended margins
in all cases, as always documented.heatmap() evaluated its add.expr argument
in the wrong environment. ()require() etc now give the correct entry of
lib.loc in the warning about an old version of a package
masking a newer required one.[] or [[]]. (Reported by Lukas Stadler;
additional fixes included as well).as.data.frame.vector(*, row.names=*) no longer produces
‘corrupted’ data frames from row names of incorrect length, but rather
warns about them. This will become an error.url connections with method = "libcurl"
are destroyed properly. ()withCallingHandler() now (again) handles warnings even
during S4 generic’s argument evaluation. ()deparse(..., control = "quoteExpressions") incorrectly
quoted empty expressions. ()format()ting datetime objects
("POSIX[cl]?t") could segfault or recycle wrongly. ()plot.ts(<matrix>, las = 1) now does use
las.saveRDS(*, compress = "gzip") now works as documented.
()Rgui front end did not always
initialize the console properly, and could cause R to crash. ()dummy.coef.lm() now works in more cases, thanks to a
proposal by Werner Stahel (). In addition, it now works for multivariate
linear models ("mlm", ) thanks to a proposal by Daniel
Wollschlaeger.as.hclust() method for "dendrogram"s
failed often when there were ties in the heights.reorder() and midcache.dendrogram() now
are non-recursive and hence applicable to somewhat deeply nested
dendrograms, thanks to a proposal by Suharto Anggono in .cor.test() now calculates very small p values more
accurately (affecting the result only in extreme not statistically
relevant cases). ()smooth(*, do.ends=TRUE) did not always work correctly
in R versions between 3.0.0 and 3.2.3.pretty(D) for date-time objects D now also
works well if range(D) is (much) smaller than a second. In
the case of only one unique value in D, the pretty range
now is more symmetric around that value than previously.pretty(dt) no longer returns a length 5 vector
with duplicated entries for Date objects dt
which span only a few days.?points were
accidentally damaged, and did not appear in R 3.2.3. ()available.packages() sometimes deleted the wrong file
when cleaning up temporary files. ()X11() device sometimes froze on Red Hat Enterprise
Linux 6. It now waits for MapNotify events instead of
Expose events, thanks to Siteshwar Vashisht. ()[dpqr]nbinom(*, size=Inf, mu=.) now works as limit
case, for ‘dpq’ as the Poisson. ()pnbinom() no longer loops infinitely in border cases.approxfun(*, method="constant") and hence
ecdf() which calls the former now correctly “predict”
NaN values as NaN.summary.data.frame() now displays NAs in
Date columns in all cases. ()CHANGES IN R 3.2.3
NEW FEATURES
Rgui.exe, Rterm.exe and
Rscript.exe. This should allow win.version()
and Sys.info() to report the actual Windows version up to
Windows 10."wininet" FTP first tries EPSV / PASV mode
rather than only using active mode (reported by Dan Tenenbaum).which.min(x) and which.max(x) may be much
faster for logical and integer x and now also work for long
vectors.tools::texi2dvi() has been
somewhat enhanced, including supporting quiet = TRUE. It
can be selected by texi2dvi = "emulation". (Windows) MiKTeX
removed its texi2dvi.exe command in Sept 2015:
tools::texi2dvi() tries texify.exe if it is
not found.Rgui.exe. (Request of .)loess(..., iterTrace=TRUE) now provides diagnostics for
robustness iterations, and the print() method for
summary(<loess>) shows slightly more.View() now displays nested data frames in a more
friendly way. (Request with patch in .)INSTALLATION and INCLUDED SOFTWARE
libintl has been
updated to that from gettext version 0.19.5.1 — this should
only affect how an external library is detected (and the only known
instance is under OpenBSD). (Wish of .)configure has a new argument –disable-java
to disable the checks for Java.configure default for MAIN_LDFLAGS has
been changed for the FreeBSD, NetBSD and Hurd OSes to one more likely to
work with compilers other than gcc (FreeBSD 10 defaults to
clang).configure now supports the OpenMP flags
-fopenmp=libomp (clang) and -qopenmp (Intel
C).configure when detecting OpenMP: see file
config.site.texi2dvi.exe. See file
MkRules.dist.BUG FIXES
regexpr(pat, x, perl = TRUE) with Python-style named
capture did not work correctly when x contained
NA strings. ()ToothGrowth has been
improved/corrected. ()model.tables(type = "means") and hence
TukeyHSD() now support "aov" fits without an
intercept term. ()close() now reports the status of a pipe()
connection opened with an explicit open argument. ()Rscript or R -f could result in attempting to
close the input file twice, possibly crashing the process. ()Sys.info() was out of step with
win.version() and did not report Windows 8.topenv(baseenv()) returns baseenv() again
as in R 3.1.0 and earlier. This also fixes compilerJIT(3)
when used in .Rprofile.detach()ing the methods package keeps
.isMethodsDispatchOn() true, as long as the methods
namespace is not unloaded.configure about the
preprocessor not finding header files. ()rchisq(*, df=0, ncp=0) now returns 0
instead of NaN, and dchisq(*, df=0, ncp=*)
also no longer returns NaN in limit cases (where the limit
is unique). ()pchisq(*, df=0, ncp > 0, log.p=TRUE) no longer
underflows (for ncp > ~60).nchar(x, "w") returned -1 for characters it did not
know about (e.g. zero-width spaces): it now assumes 1. It now knows
about most zero-width characters and a few more double-width
characters.which.min() is now more precise about behavior
with logical arguments. ()"latin1"
or "bytes" was in some cases computed incorrectly.abbreviate() did not give names to the return value if
minlength was zero, unlike when it was positive.dir.create() did not always warn when it
failed to create a directory. ()grep() and related functions did not
handle UTF-8 strings properly. ()read.dcf() sometimes misread lines longer than 8191
characters. (Reported by Hervé Pagès with a patch.)within(df, ..) no longer drops columns whose name start
with a ".".HTTP server converted entire
Content-Type to lowercase including parameters which can
cause issues for multi-part form boundaries ().splineDesign(*, outer.ok=TRUE) (splines) is
better now (), and interpSpline() now allows
sparse=TRUE for speedup with non-small sizes.traceback() did not report the source line number. (Patch
by Kirill Müller.)options("deparse.max.lines") set. ()bs(*, Boundary.knots=) had boundary knots inside
the data range, extrapolation was somewhat off. (Patch by Trevor
Hastie.)var() and hence sd() warn about
factor arguments which are deprecated now. ()loess(*, weights = *) stored wrong weights and hence
gave slightly wrong predictions for newdata. ()aperm(a, *) now preserves
names(dim(a)).poly(x, ..) now works when either raw=TRUE
or coef is specified. ()data(package=*) is more careful in determining the
path.prettyNum(*, decimal.mark, big.mark): fixed bug
introduced when fixing .CHANGES IN R 3.2.2
SIGNIFICANT USER-VISIBLE CHANGES
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 ftp: sites being inaccessible under the new
default method (but the previous methods remain available).
NEW FEATURES
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 .)
(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:// URLs 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).
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.
C-LEVEL FACILITIES
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).INSTALLATION and INCLUDED SOFTWARE
libtool script generated by configure
has been modified to support FreeBSD >= 10 ().BUG FIXES
na.action argument was used in
model.frame(), the original data could be modified. ()getGraphicsEvent() could cause a crash if a graphics
window was closed while it was in use. ()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 .)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 .download.packages() failed for type equal
to either "both" or "binary". (Reported by Dan
Tenenbaum.)dendrogram method of labels() is much
more efficient for large dendrograms, now using rapply().
(Comment #15 of )"port" algorithm of nls() could give
spurious errors. (Reported by Radford Neal.).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.
()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. ()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(). (, )getClass("foo") now also returns a class definition
when it is found in the cache more than once.CHANGES IN R 3.2.1
NEW FEATURES
utf8ToInt() 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
nzchar() in general and nchar() in the R 3.2.x
series, the default remains FALSE which is fully back
compatible. From R 3.3.0, nchar()’s 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.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.BUG FIXES
acf() and ccf() now guarantee values
strictly in (instead of sometimes very slightly outside). .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.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).–clean option to
R CMD INSTALL could fail. ()choose.files() would occasionally
include characters from the result of an earlier call in the result of a
later one. ()RSiteSearch() in R 3.2.0 caused it to
submit invalid URLs. ()Rscript and command line R silently
ignored incomplete statements at the end of a script; now they are
reported as parse errors. ()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.
()install.packages(type = "both") and related functions could
repeatedly query the user for it. (Part of ).rowSums() etc. did not check
the length of their argument, so could segfault. ()quietly argument of library() is now
correctly propagated from .getRequiredPackages2().-llzma to be
omitted from the main link.!, & and |, now give correct
error messages when appropriate, e.g., for ‘&‘(TRUE) or
‘!‘(). ()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. ()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 ) computes estimated variances
based on a the number of effective observations as in R version 3.0.1
and earlier. ()slotNames(.) is now correct for
"signature" objects (mostly used internally in
methods).NA.CHANGES IN R 3.2.0
NEW FEATURES
anyNA() 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.
()
(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 )
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. ()
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 .)
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 .
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.
()
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 .
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.)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 or more
elements. (For cbind(), wish of .)
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 , 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 ).
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 .
INSTALLATION and INCLUDED SOFTWARE
donttest sections of R’s help files can be tested
bymake check TEST_DONTTEST=TRUE .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 .)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.UTILITIES
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:
README.md file can be processed: this needs
pandoc installed.DESCRIPTION, CITATION, NEWS.Rd
and README.md files and in the help files (provided the
build has libcurl support).DESCRIPTION file.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.
C-LEVEL FACILITIES
logspace_sum(logx[], n).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.R_allocLD, like R_alloc
but guaranteed to have sufficient alignment for long double
pointers.isPairList() now returns TRUE for
DOTSXP.WINDOWS BUILD CHANGES A number of changes to the Windows build system are in development. The following are currently in place.
make target rsync-extsoft has been
added to obtain copies of the external libraries from CRAN.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.PACKAGE INSTALLATION
(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").
DEPRECATED AND DEFUNCT
download.file(method = "lynx") is defunct.zlib,
bzip2, xz and PCRE is deprecated: these are
frozen (bar essential bug-fixes) and will be removed for R 3.3.0.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.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.BUG FIXES
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.missing() when arguments are propagated through
... . ()eigen(m) now defaults to symmetric = TRUE
even when the dimnames are asymmetric if the matrix is otherwise
symmetric. ()... through
callGeneric() and callNextMethod(). ()callGeneric() now works after a
callNextMethod().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.qbeta() the inversion of pbeta() is
much more sophisticated. This works better in corner cases some of which
failed completely previously (), or were using too many iterations.kmeans(x, k) would fail when
nrow(x) >= 42949673. (Comment 6 of )CHANGES IN R 3.1.3
NEW FEATURES
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.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. ()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 )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).install.packages(type = "both") and the appropriate type
and repos = NULL will be inferred.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.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.INSTALLATION and INCLUDED SOFTWARE
configure accepts MAKEINFO=texi2any as
another way to ensure texinfo 5.x is used when both 5.x and 4.x
are installed.UTILITIES
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.DEPRECATED AND DEFUNCT
configure option
–with-valgrind-instrumentation=3 is deprecated and will be
removed in R 3.2.0.BUG FIXES
Rscript.exe was missing a manifest
specifying the modern style for common controls (e.g., the download
progress bar).qr.Q() failed on complex arguments due to pre-3.0(!)
typo. ()abs() failed with named arguments when the argument was
complex. ()"noquote" objects may now be used as columns in data
frames. ()0.0e50000) could give NaN. ()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. ()Rgui.exe messed up
the console. ()choose.files() command returned a blank
string when the user asked for a single file but cancelled the request.
()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.)substr()
and its replacement version have been avoided. Inter alia that
fix gives the documented behaviour for
substr(x, 1, 2) <- "" (subsequently reported as ).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. ()tools:::.Rdconv() didn’t accept –encoding=
due to a typo. ()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. ()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. ()RShowDoc("NEWS", "txt") had not been updated for the
layout changes of R 3.1.0.xtfrm() method for class "Surv" has
been corrected and its description expanded.mode(x) <- y would incorrectly evaluate
x before changing its mode. ()besselJ(1, 2^64) and besselY(..) now
signal a warning, returning NaN instead of typically
segfaulting. (Issue 3 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 3.1.2
NEW FEATURES
embedFonts() 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.[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).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).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.setRepositories()
now defaults to 3.0. (It can be set at runtime via
environment variable R_BIOC_VERSION.)setRepositories(). It has no binary packages
available for R 3.1.x and those for earlier versions were 32-bit
only.INSTALLATION and INCLUDED SOFTWARE
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.-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 .)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.)UTILITIES
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.BUG FIXES
dmultinom() did not handle non-finite probabilities
correctly.prettyNum(x, zero.print=*) now also works when
x contains NAs.nlminb() on Windows was
traced to a compiler bug in gcc 4.6.3; a workaround has been put in
place. ( and ).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. ()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. ().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.list(‘ab‘ = 1) now print
correctly.getAnywhere("C_pbinom") now returns correctly a single
object (rather than unlisting it).confint() method for nls() fits failed
it these has specified parameter limits despite using an algorithm other
than "port". ()initialize() method.removeSource() did not properly handle expressions
containing arguments that were supplied as missing,
e.g. x[i,]. ()as.environment(list()) now works, and
as.list() of such an environment is now the same as
list(). ()options(list()) now works (trivially). ()merge(<dendrogram>, ..) now works correctly for
two ‘independent’ dendrograms (), and still compatibly via
adjust = "auto" e.g. for two branches of an existing
dendrogram.plot method for "hclust" objects gets
an optional argument check; when that is true (the default)
it checks more carefully for valid input.bin/R and bin/Rscript executables failed
to run. ()Rscript no longer passes –args to
R when there are no extra (“user”) arguments.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. ()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. ()RShowDoc("NEWS") now displays the PDF version.plot.histogram() and hence hist() now
respect the xaxs, yaxs and lab
graphics parameters. ()bw.SJ(x) and other bw.*() no longer segfault when
x contains non-finite values. ()R CMD Rd2pdf unintentionally ignored its
–os option.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).CHANGES IN R 3.1.1
NEW FEATURES
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.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.)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.smooth.spline() is now exported, as
.nknots.smspl().dbeta(, a,b), pbeta(),
qbeta() and rbeta() are now defined also for ,
, or infinite and (where they typically returned NaN
before).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.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.$
operator on data frames is now only given when
options("warnPartialMatchDollar") is
TRUE.package?foo now try the
package foo whether loaded or not.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).INSTALLATION and INCLUDED SOFTWARE
configure option –with-internal-tzcode can
now be used with variable rsharedir.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.R CMD check) in the ‘Writing R Extensions’ manual.src/extra/xz inconsistently (and apparently in some cases
incorrectly), so it has been simplified. ()BUG FIXES
dbinom(x, n), pbinom(),
dpois(), etc, are slightly less restrictive in checking if
n is integer-valued. (Wish of .)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 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. ()strptime() rejected time-zone
offsets of more than +1200 (+1245,
+1300 and +1400 can occur). ()png(type = "cairo", antialias = "gray")
was not accepted. ()save(..., envir=) with named objects could fail.
()Sweave() mis-parsed Sexpr expressions that
contained backslashes. ()options(foo = NULL) was not the
previous value of the option. ()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”."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").dev2bitmap() and
bitmap() was truncated to 1000 characters: modern versions
of GhostScript on most platforms have many more devices.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 .)chull() with non-finite
points now give an error (related to ).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.0x110p-5L which were
incorrectly qualified by L were parsed incorrectly since R
3.0.0, with a slightly garbled warning. ()system() returned success on some platforms even if the
system was unable to launch a process. ()Rgui console.) Unbuffered output was sometimes
not output immediately if the prompt was not on the last line of the
console.DESCRIPTION or other text files to be the package encoding,
so non-ASCII characters could be displayed incorrectly.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.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.)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()."help.try.all.packages" option was ignored when the
shortcut syntax for help was used, e.g. ?foo.sort() and
D() have been fixed. (Found by Radford Neal.)numericDeriv() sometimes miscalculated the gradient. (,
reported originally by Radford Neal)CHANGES IN R 3.1.0
NEW FEATURES
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 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 .)
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
.)
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 .)
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 .)
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 .)
colSums() and friends now have support for arrays
and data-frame columns with 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. ()
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 .
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 tate pace initialization which has been observed to be more
reliable close to non-stationarity: see .
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. ()
sort.list(method = "radix") now allows negative
integers (wish of ).
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 .)
The handling of DF[i,] <- a where i
is of length 0 is improved. (Inter alia, fixes .)
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().
INSTALLATION and INCLUDED SOFTWARE
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
.)
PACKAGE INSTALLATION
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, 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.
DEBUGGING
browser() are now consistent with calls to the
browser triggered by debug(), in that will default to
n rather than c.s has been added, to “step into”
function calls.f has been added, to “finish” the
current loop or function.help will display a
short list of available commands.UTILITIES
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. 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.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_.tools::texi2dvi() limits the number of
passes tried to 20.C-LEVEL FACILITIES
R_WaitEvent() has been added
(with declaration in headerR.h) to block execution until
the next event is received by R.Rmath.h header can be suppressed by
defining R_NO_REMAP_RMATH.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.prec() to
fprec() in header Rmath.h has been
removed.ZGESDD and
ZGELSD.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().)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.DEPRECATED AND DEFUNCT
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.$ 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]].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.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).R_OSX_VALGRIND has been
removed: it is not needed in current valgrind.BUG FIXES
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).‘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. ()nls() with no start argument may now work
inside another function (scoping issue).pbeta() and similar work better for very large
(billions) ncp.localtime changed the
tzname variables the reported abbreviation could have been
that of the last time converted.all.equal(list(1), identity) now works.git repository. This allows R to be installed on some
platforms for which this was a blocker ( suggests Linux on ARM and
HP-UX).? applied to a call to an S4 generic failed in several
cases. ()... in
their argument list were incorrect. ()methods::callGeneric(). ()aggregrate() in introduced a new bug in
the case of no grouping variables. ()as.dendrogram() was hidden
accidentally, (), and order.dendrogram(d) gave too much for
a leaf d. ()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. ()printCoefmat() called from quite a few
print() methods now obeys small
getOption("width") settings, line wrapping the
"signif. codes" legend appropriately. ()model.matrix() assumed that the stored dimnames for a
matrix was NULL or length 2, but length 1 occurred.CHANGES IN R 3.0.3
NEW FEATURES
.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 or more elements,
for those with large amounts of patience and disc space.La_version(), to report the
version of LAPACK in use.doc/manual/Makefile. Suggested by Mauro Cavalcanti.)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.‘“. ()read.table(), readLines() and
scan() now warn when an embedded nul is found in the input.
(Related to which was puzzled by the behaviour in this unsupported
case.)file.symlink() works around the
undocumented restriction of the Windows system call to backslashes.
(Wish of .)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: .)options() and (C-level) path.expand()
re-entrantly).INSTALLATION and INCLUDED SOFTWARE
VT and hence agrees with
POSIX’s.PACKAGE INSTALLATION
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.C-LEVEL FACILITIES
rround() to
Rf_fround() in header Rmath.h is now formally
deprecated: use fround() directly.prec() and trunc() in the
Rmath.h header has been disabled in C++ code (it has caused
breakage with libc++ headers).BUG FIXES
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.
()rbind() and cbind() did not handle list
objects correctly. ()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. ( and )min() did not handle NA_character_ values
properly. (Reported by Magnus Thor Torfason.)readRegistry() would duplicate default
values for keys. ()str(..., strict.width = "cut") did not handle it
properly when more than one line needed to be cut. (Reported by Gerrit
Eichner.)aggregate() could fail when there were too many levels
present in the by argument. ()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. ()contour() could fail when dealing with extremely small
z values. ()browseEnv(), format(),
gl(), relist() and
summary.data.frame(). (E.g., )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.)parse() (and
thus source()) to segfault. ()nmax = 1 in
duplicated() or unique() is now silently
ignored.qcauchy(p, *) is now fully accurate even when p is very
close to 1. ()validmu() and valideta() functions in
the standard glm() families now also report non-finite
values, rather than failing..Rout.save file) were not
being compared to the new ones during R CMD check.tk_select.list() no longer
causes the window to close. ()parallel::splitindices(). ()help.search() and
?? sometimes contained badly constructed links.c() and related functions such as unlist()
converted raw vectors to invalid logical vectors. ()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.)bmp() device was not recording
res = NA correctly: it is now recorded as 72 ppi.clang compiler.hcl() now honours NA inputs (previously
they were mapped to black).NA
returned that time. (The platforms affected include Linux and OS X, but
not Windows nor Solaris.)rowsum() has more support for matrices and data frames
with or more elements. ()predict(<lm object>, interval = "confidence", scale = <something>)
now works. ()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. (, patch based on code submitted by
Alex Bertram.)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)
stack imbalance.KalmanRun() did not
take missing values into account.%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. ()approx() and approxfun() now handle
infinite values with the "constant" method. ()stripchart() again respects reversed limits in
xlim and ylim. ()CHANGES IN R 3.0.2
NEW FEATURES
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 (necessarily summing more than 4
million elements).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 .col2rgb() now converts factors to character strings not
integer codes (suggested by Bryan Hanson).tail(warnings()) now works, via the new
‘[‘ method.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.tools::getVignetteInfo() function has been added to
give information about installed vignettes.assertCondition(), etc. utilities in
tools, useful for testing.BUILTIN functions.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..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.parse() finds a syntax error, it now makes partial
parse information available up to the location of the error. (Request of
Reijo Sund.)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. ()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 .)formatC(x) no longer copies the class of x
to the result, to avoid misuse creating invalid objects as in . A
warning is given if a class is discarded.npk has been copied from to allow more tests to
be run without recommended packages being installed.arima() has been changed and in some
examples avoids a local maximum. ()termplot() now has an argument transform.x
to control the display of individual terms in the plot. ()format() now supports digits = 0, to
display nsmall decimal places.par() parameter called
"page", which returns a logical value indicating whether
the next plot.new() call will start a new page.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.UTILITIES
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
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
Depends,
Imports, Suggests and Enhances
fields of the DESCRIPTION file.Imports but not imported from,
neither in the NAMESPACE file nor using the ::
nor ::: operators.library() or
requires() calls in the R code but were already put on the
search path via Depends.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.::: calls where
:: would do.:: which are not exported.::: 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.
INSTALLATION and INCLUDED SOFTWARE
texinfo 5.x.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.zlib has been updated to 1.2.8,
a bug-fix release.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.–disable-byte-compilation will
override the DESCRIPTION files of recommended packages,
which typically require byte-compilation.TMPDIR is set to a path containing spaces, but this is not
recommended and external software (such as texi2dvi) may
fail.PACKAGE INSTALLATION
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.BSD is deprecated: use
BSD_3_clause or BSD_2_clause instead. License
X11 is deprecated: use MIT or
BSD_2_clause instead.LinkingTo packages are now
recognized: they are checked at installation. (Fields with version
requirements were previously silently ignored.)S3method entries in a
NAMESPACE file has been removed.2.13, but this can be set by the
environment variable R_BIOC_VERSION when R is
installed.C-LEVEL FACILITIES
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.DEPRECATED AND DEFUNCT
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.readNEWS() and checkNEWS() in
package tools are deprecated (and they have not worked with
current NEWS files for a long time).DOCUMENTATION
BUG FIXES
help.request() could not determine the current version
of R on CRAN. ()file.info() failed on root directories
unless the path was terminated with an explicit ".".
()regmatches<-() replacement function mishandled
results coming from regexpr(). ()setClass() and
representation() still suggested the deprecated argument
representation=. ()R CMD config failed in an installed build of R 3.0.1
(only) when a sub-architecture was used. (Reported by Berwin
Turlach.)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.)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. ()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.)ZHER2K in the reference BLAS had a
comment-out bug in two places. This caused trouble with
eigen() for Hermitian matrices. ( and report from Robin
Hankin)vignette() and browseVignettes() did not
display non-Sweave vignettes properly.: operator.
(Found by Radford Neal; , )svd() returned NULL rather than omitting
components as documented. (Found by Radford Neal; )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. ()deparse() now deparses raw vectors in a form that is
syntactically correct. ()jpeg driver in Sweave created a JPEG file, but gave
it a .png extension. ()mget(), seq.int() and
numericDeriv() did not duplicate arguments properly. (, ,
)kmeans(algorithm = "Hartigan-Wong") now always stops
iterating in the QTran stage. ().read.dcf() re-allocated incorrectly and so could
segfault when called on a file with lines of more than 100 bytes.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, ).stem() now discards infinite inputs rather than
hanging. ()0x1.1p0), rather than returning unintended
values for malformed constants. ()model.matrix() now works with very long LHS names (more
than 500 bytes). ()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 0. ()+ 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. ()–without-recommended-packages.source() did not display filenames when reporting
syntax errors.R (instead of
Rterm or Rgui) would lose any zero-length
strings from the command line arguments. ()–encoding=foo were not handled properly. ()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. ()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.)lgamma(-x) is no longer NaN for very small
x.system2() now respects specifying
stdout and stderr as files if called from
Rgui. ()x11() device whilst locator()
or identify() is in progress no longer hangs R. ()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.tools::Rd2txt_options(itemBullet=)
was not respected in some locales. ()mcMap() was not exported by package parallel.
()plot() for TukeyHSD objects did not
balance dev.hold() and dev.flush() calls on
multi-page plots. ()CHANGES IN R 3.0.1
NEW FEATURES
chooseCRANmirror() 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.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.pairs() gains a line.main option for title
placement.UTILITIES
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.
PACKAGE INSTALLATION
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.BUG FIXES
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 ().str(d) no longer gives an error when
names(d) contain illegal multibyte strings ().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 ().read.table() misread some files that
contained quote characters ().cat() with sep a character vector of
length greater than one and more than one argument was using separators
inconsistently ().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 ).identify() and locator() did
not record information correctly, so replaying a graph (e.g., by copying
it to another device) would fail. ()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 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. ()parallel::mclapply(mc.preschedule = TRUE) was a list of
strings and not of error objects. (Spotted by Karl Forner and Bernd
Bischl.)help() found multiple pages with the
same alias, the HTML display of all the selections was not produced.
()splinefun(method="monoH.FC") now produces a function
with first argument named x and allows
deriv=3, as documented. ()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. ()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.)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. ()CHANGES IN R 3.0.0
SIGNIFICANT USER-VISIBLE CHANGES
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.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.NEW FEATURES
identical() has a new argument,
ignore.environment, used when comparing functions (with
default FALSE as before).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.layout(), the limits on the grid size have been
raised (again).provideDimnames() utility function.length() return a double value which
is representable as an integer (as often happens for package ), this is
converted to an integer.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.)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.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.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, .)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.sort() method has been added for
"bibentry" objects.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 .)split() gains a sep argument.termplot() does a better job when given a model with
interactions (and no longer attempts to plot interaction terms).getParseData() and getParseText() access the
data.rep_len() analogous to
rep.int() for when speed is required (and names are
not).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.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 .)optimize() and uniroot() no longer use a
shared parameter object across calls. (nlm(),
nlminb() and 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.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.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.chol() and
solve()) accept logical matrices (and coerce to
numeric).sample.int() has some support for : 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..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.)%~% 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, .)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.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).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."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.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."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.srcfile argument to parse() may now be
a character string, to be used in error messages.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.utils::process.events() function has been added to
trigger immediate event handling.Sys.which() now returns NA (not
"") for NA inputs (related to ).print() method for class "htest" gives
fewer trailing spaces (wish of ). 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 .)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.?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.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
options("keep.source").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 in
Unix.Rprof() now optionally records
information about time spent in GC.options(stringsAsFactors = FALSE),
model.frame(), model.matrix() and
replications() now automatically convert character vectors
to factors without a warning.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 .)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.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_GC_MEM_GROW. See ?Memory for more
details.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..Device and .Devices no longer includes the
file name. This is for consistency with other platforms and was
requested by the maintainer. win.metafile() still uses the
file name: the exact form is used by package .set.seed(NULL) re-initializes .Random.seed
as 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).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.LONG VECTORS This section applies only to 64-bit platforms.
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 or more by the replacement function with a double
value.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).R_alloc can now allocate or more
bytes.agrep() and grep() will return double
vectors of indices for long vector inputs..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).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.PERFORMANCE IMPROVEMENTS
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.
PACKAGE INSTALLATION
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 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.
UTILITIES
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.
DEPRECATED AND DEFUNCT
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,
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.
CODE MIGRATION
.Internal() calls)..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)..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()).PACKAGE parallel
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.R_PARALLEL_PORT to
10187.C-LEVEL FACILITIES
Rinternals.h no longer includes the
non-API header R_exts/PrtUtil.h, and that no longer
includes R_exts/Print.h.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.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.Rf_, notably [dpq]nbinom_mu.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.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.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.REPROTECT macro now checks that the protect index
is valid.chol,
chol2inv, cg, ch and
rg, and the C entry points Brent_fmin,
fft_factor and fft_work..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).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).INTERNATIONALIZATION
?tools::update_pkg_po.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..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.)INSTALLATION
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).etc/javaconf for subsequent use by
R CMD javareconf.makeinfo version 5.0 (which
requires a slightly different .texi syntax).–use-system-zlib and
–use-system-pcre are now tested as 1.2.5 and 8.10
respectively.configure no longer looks for file
~/.Rconfig: ~/.R/config has long been
preferred.BUG FIXES
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. ()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).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(),
tools::parseLatex() and tools::parse_Rd() were
not reentrant, leading to errors in rare circumstances such as a garbage
collection triggering a recursive call.$<- 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.
()NEWS.Rd file, the main HTML package
index page did not link to it. (Reported by Dirk Eddelbuettel.)@<- 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). ()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.cat() on a malformed UTF-8 string could cause
the Windows GUI to lock up. ()removeClass(cc) gave "node stack overflow" for some
class definitions containing "array" or
"matrix".CHANGES in previous versions
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 doc/html/NEWS.2.html.