The build system rolled up R-3.5.0.tar.gz (codename "Joy in Playing")
this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.5.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case
you wish
to check that they are uncorrupted:
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R-3/R-3.5.0.tar.gz
This is the relevant part of the NEWS file
CHANGES IN R 3.5.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* All packages are by default byte-compiled on installation. This
makes the installed packages larger (usually marginally so) and
may affect the format of messages and tracebacks (which often
exclude .Call and similar).
NEW FEATURES:
* factor() now uses order() to sort its levels, rather than
sort.list(). This allows factor() to support custom vector-like
objects if methods for the appropriate generics are defined. It
has the side effect of making factor() succeed on empty or
length-one non-atomic vector(-like) types (e.g., "list"), where
it failed before.
* diag() gets an optional names argument: this may require updates
to packages defining S4 methods for it.
* chooseCRANmirror() and chooseBioCmirror() no longer have a
useHTTPS argument, not needed now all R builds support https://
downloads.
* New summary() method for warnings() with a (somewhat
experimental) print() method.
* (methods package.) .self is now automatically registered as a
global variable when registering a reference class method.
* tempdir(check = TRUE) recreates the tempdir() directory if it is
no longer valid (e.g. because some other process has cleaned up
the /tmp directory).
* New askYesNo() function and "askYesNo" option to ask the user
binary response questions in a customizable but consistent way.
(Suggestion of PR#17242.)
* New low level utilities ...elt(n) and ...length() for working
with ... parts inside a function.
* isTRUE() is more tolerant and now true in
x <- rlnorm(99)
isTRUE(median(x) == quantile(x)["50%"])
New function isFALSE() defined analogously to isTRUE().
* The default symbol table size has been increased from 4119 to
49157; this may improve the performance of symbol resolution when
many packages are loaded. (Suggested by Jim Hester.)
* line() gets a new option iter = 1.
* Reading from connections in text mode is buffered, significantly
improving the performance of readLines(), as well as scan() and
read.table(), at least when specifying colClasses.
* order() is smarter about picking a default sort method when its
arguments are objects.
* available.packages() has two new arguments which control if the
values from the per-session repository cache are used (default
true, as before) and if so how old cached values can be to be
used (default one hour).
These arguments can be passed from install.packages(),
update.packages() and functions calling that: to enable this
available.packages(), packageStatus() and download.file() gain a
... argument.
* packageStatus()'s upgrade() method no longer ignores its ...
argument but passes it to install.packages().
* installed.packages() gains a ... argument to allow arguments
(including noCache) to be passed from new.packages(),
old.packages(), update.packages() and packageStatus().
* factor(x, levels, labels) now allows duplicated labels (not
duplicated levels!). Hence you can map different values of x to
the same level directly.
* Attempting to use names<-() on an S4 derivative of a basic type
no longer emits a warning.
* The list method of within() gains an option keepAttrs = FALSE for
some speed-up.
* system() and system2() now allow the specification of a maximum
elapsed time ('timeout').
* debug() supports debugging of methods on any object of S4 class
"genericFunction", including group generics.
* Attempting to increase the length of a variable containing NULL
using length()<- still has no effect on the target variable, but
now triggers a warning.
* type.convert() becomes a generic function, with additional
methods that operate recursively over list and data.frame
objects. Courtesy of Arni Magnusson (PR#17269).
* lower.tri(x) and upper.tri(x) only needing dim(x) now work via
new functions .row() and .col(), so no longer call as.matrix() by
default in order to work efficiently for all kind of matrix-like
objects.
* print() methods for "xgettext" and "xngettext" now use
encodeString() which keeps, e.g. "\n", visible. (Wish of
PR#17298.)
* package.skeleton() gains an optional encoding argument.
* approx(), spline(), splinefun() and approxfun() also work for
long vectors.
* deparse() and dump() are more useful for S4 objects, dput() now
using the same internal C code instead of its previous imperfect
workaround R code. S4 objects now typically deparse perfectly,
i.e., can be recreated identically from deparsed code.
dput(), deparse() and dump() now print the names() information
only once, using the more readable (tag = value) syntax, notably
for list()s, i.e., including data frames.
These functions gain a new control option "niceNames" (see
.deparseOpts()), which when set (as by default) also uses the
(tag = value) syntax for atomic vectors. On the other hand,
without deparse options "showAttributes" and
"niceNames", names
are no longer shown also for lists. as.character(list( c (one 1)))
now includes the name, as as.character(list(list(one = 1)))
has always done.
m:n now also deparses nicely when m > n.
The "quoteExpressions" option, also part of "all", no
longer
quote()s formulas as that may not re-parse identically.
(PR#17378)
* If the option setWidthOnResize is set and TRUE, R run in a
terminal using a recent readline library will set the width
option when the terminal is resized. Suggested by Ralf Goertz.
* If multiple on.exit() expressions are set using add = TRUE then
all expressions will now be run even if one signals an error.
* mclapply() gets an option affinity.list which allows more
efficient execution with heterogeneous processors, thanks to
Helena Kotthaus.
* The character methods for as.Date() and as.POSIXlt() are more
flexible _via_ new arguments tryFormats and optional: see their
help pages.
* on.exit() gains an optional argument after with default TRUE.
Using after = FALSE with add = TRUE adds an exit expression
before any existing ones. This way the expressions are run in a
first-in last-out fashion. (From Lionel Henry.)
* On Windows, file.rename() internally retries the operation in
case of error to attempt to recover from possible anti-virus
interference.
* Command line completion on :: now also includes lazy-loaded data.
* If the TZ environment variable is set when date-time functions
are first used, it is recorded as the session default and so will
be used rather than the default deduced from the OS if TZ is
subsequently unset.
* There is now a [ method for class "DLLInfoList".
* glm() and glm.fit get the same singular.ok = TRUE argument that
lm() has had forever. As a consequence, in glm(*, method
<your_own>), user specified methods need to accept a singular.ok
argument as well.
* aspell() gains a filter for Markdown (.md and .Rmd) files.
* intToUtf8(multiple = FALSE) gains an argument to allow surrogate
pairs to be interpreted.
* The maximum number of DLLs that can be loaded into R e.g. _via_
dyn.load() has been increased up to 614 when the OS limit on the
number of open files allows.
* Sys.timezone() on a Unix-alike caches the value at first use in a
session: _inter alia_ this means that setting TZ later in the
session affects only the _current_ time zone and not the _system_
one.
Sys.timezone() is now used to find the system timezone to pass to
the code used when R is configured with --with-internal-tzcode.
* When tar() is used with an external command which is detected to
be GNU tar or libarchive tar (aka bsdtar), a different
command-line is generated to circumvent line-length limits in the
shell.
* system(*, intern = FALSE), system2() (when not capturing output),
file.edit() and file.show() now issue a warning when the external
command cannot be executed.
* The "default" ("lm" etc) methods of vcov() have gained
new
optional argument complete = TRUE which makes the vcov() methods
more consistent with the coef() methods in the case of singular
designs. The former (back-compatible) behavior is given by
vcov(*, complete = FALSE).
* coef() methods (for lm etc) also gain a complete = TRUE optional
argument for consistency with vcov().
For "aov", both coef() and vcov() methods remain back-compatibly
consistent, using the _other_ default, complete = FALSE.
* attach(*, pos = 1) is now an error instead of a warning.
* New function getDefaultCluster() in package parallel to get the
default cluster set via setDefaultCluster().
* str(x) for atomic objects x now treats both cases of is.vector(x)
similarly, and hence much less often prints "atomic". This is a
slight non-back-compatible change producing typically both more
informative and shorter output.
* write.dcf() gets optional argument useBytes.
* New, partly experimental packageDate() which tries to get a valid
"Date" object from a package DESCRIPTION file, thanks to
suggestions in PR#17324.
* tools::resaveRdaFiles() gains a version argument, for use when
packages should remain compatible with earlier versions of R.
* ar.yw(x) and hence by default ar(x) now work when x has NAs,
mostly thanks to a patch by Pavel Krivitsky in PR#17366. The
ar.yw.default()'s AIC computations have become more efficient by
using determinant().
* New warnErrList() utility (from package nlme, improved).
* By default the (arbitrary) signs of the loadings from princomp()
are chosen so the first element is non-negative.
* If --default-packages is not used, then Rscript now checks the
environment variable R_SCRIPT_DEFAULT_PACKAGES. If this is set,
then it takes precedence over R_DEFAULT_PACKAGES. If default
packages are not specified on the command line or by one of these
environment variables, then Rscript now uses the same default
packages as R. For now, the previous behavior of not including
methods can be restored by setting the environment variable
R_SCRIPT_LEGACY to yes.
* When a package is found more than once, the warning from
find.package(*, verbose=TRUE) lists all library locations.
* POSIXt objects can now also be rounded or truncated to month or
year.
* stopifnot() can be used alternatively via new argument exprs
which is nicer and useful when testing several expressions in one
call.
* The environment variable R_MAX_VSIZE can now be used to specify
the maximal vector heap size. On macOS, unless specified by this
environment variable, the maximal vector heap size is set to the
maximum of 16GB and the available physical memory. This is to
avoid having the R process killed when macOS over-commits memory.
* sum(x) and sum(x1,x2,..,x<N>) with many or long logical or
integer vectors no longer overflows (and returns NA with a
warning), but returns double numbers in such cases.
* Single components of "POSIXlt" objects can now be extracted and
replaced via [ indexing with 2 indices.
* S3 method lookup now searches the namespace registry after the
top level environment of the calling environment.
* Arithmetic sequences created by 1:n, seq_along, and the like now
use compact internal representations via the ALTREP framework.
Coercing integer and numeric vectors to character also now uses
the ALTREP framework to defer the actual conversion until first
use.
* Finalizers are now run with interrupts suspended.
* merge() gains new option no.dups and by default suffixes the
second of two duplicated column names, thanks to a proposal by
Scott Ritchie (and Gabe Becker).
* scale.default(x, center, scale) now also allows center or scale
to be "numeric-alike", i.e., such that as.numeric(.) coerces
them
correctly. This also eliminates a wrong error message in such
cases.
* par*apply and par*applyLB gain an optional argument chunk.size
which allows to specify the granularity of scheduling.
* Some as.data.frame() methods, notably the matrix one, are now
more careful in not accepting duplicated or NA row names, and by
default produce unique non-NA row names. This is based on new
function .rowNamesDF(x, make.names = *) <- rNms where the logical
argument make.names allows to specify _how_ invalid row names
rNms are handled. .rowNamesDF() is a "workaround" compatible
default.
* R has new serialization format (version 3) which supports custom
serialization of ALTREP framework objects. These objects can
still be serialized in format 2, but less efficiently.
Serialization format 3 also records the current native encoding
of unflagged strings and converts them when de-serialized in R
running under different native encoding. Format 3 comes with new
serialization magic numbers (RDA3, RDB3, RDX3). Format 3 can be
selected by version = 3 in save(), serialize() and saveRDS(), but
format 2 remains the default for all serialization and saving of
the workspace. Serialized data in format 3 cannot be read by
versions of R prior to version 3.5.0.
* The "Date" and "date-time" classes "POSIXlt"
and "POSIXct" now
have a working `length<-` method, as wished in PR#17387.
* optim(*, control = list(warn.1d.NelderMead = FALSE)) allows to
turn off the warning when applying the default "Nelder-Mead"
method to 1-dimensional problems.
* matplot(.., panel.first = .) etc now work, as log becomes
explicit argument and ... is passed to plot() unevaluated, as
suggested by Sebastian Meyer in PR#17386.
* Interrupts can be suspended while evaluating an expression using
suspendInterrupts. Subexpression can be evaluated with
interrupts enabled using allowInterrupts. These functions can be
used to make sure cleanup handlers cannot be interrupted.
* R 3.5.0 includes a framework that allows packages to provide
alternate representations of basic R objects (ALTREP). The
framework is still experimental and may undergo changes in future
R releases as more experience is gained. For now, documentation
is provided in <URL:
https://svn.r-project.org/R/branches/ALTREP/ALTREP.html>.
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.
* It is now possible to set 'timeouts' (elapsed-time limits) for
most parts of R CMD check _via_ environment variables documented
in the 'R Internals' manual.
* The 'BioC extra' repository which was dropped from Bioconductor
3.6 and later has been removed from 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
rmarkdown from the VignetteBuilder field.
INSTALLATION on a UNIX-ALIKE:
* Support for a system Java on macOS has been removed - install a
fairly recent Oracle Java (see 'R Installation and
Administration' SSC.3.2).
* 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.
* C99 functions 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:
* 'Writing R Extensions' documents macros MAYBE_REFERENCED,
MAYBE_SHARED and MARK_NOT_MUTABLE that should be used by package
C code instead NAMED or SET_NAMED.
* The object header layout has been changed to support merging the
ALTREP branch. This requires re-installing packages that use
compiled code.
* 'Writing R Extensions' now documents the 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).
* The declaration of 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.
* The S4 methods on 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 LL' = H + uI correctly. (PR#17249).
* An S4 method that "rematches" to its generic and overrides the
default value of a generic formal argument to 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.
* Connections are now written correctly with encoding "UTF-16LE".
(PR#16737).
* Evaluation of ..0 now signals an error. When ..1 is used and ...
is empty, the error message is more appropriate.
* (Windows mainly.) Unicode code points which require surrogate
pairs in UTF-16 are now handled. All systems should properly
handle surrogate pairs, even those systems that do not need to
make use of them. (PR#16098)
* 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. (PR#17120)
* line(x, y) now correctly computes the medians of the left and
right group's x-values and in all cases reproduces straight
lines.
* Extending S4 classes with slots corresponding to special
attributes like dim and dimnames now works.
* Fix for legend() when fill has multiple values the first of which
is NA (all colours used to default to par(fg)). (PR#17288)
* 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).
* The documentation for installed.packages(noCache = TRUE)
incorrectly claimed it would refresh the cache.
* aggregate(<data.frame>) no longer uses spurious names in some
cases. (PR#17283)
* 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 PR#17291.
* 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. (PR#17311)
* 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 PR#17300.
* Arithmetic with zero-column data frames now works more
consistently; issue raised by Bill Dunlap.
Arithmetic with data frames gives a data frame for ^ (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.
* Internal C-level 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 Matrix.
* Reverted unintended change in behavior of return calls in on.exit
expressions introduced by stack unwinding changes in R 3.3.0.
* Attributes on symbols are now detected and prevented; attempt to
add an attribute to a symbol results in an error.
* fisher.test(*, workspace = <n>) now may also increase the
internal stack size which allows larger problem to be solved,
fixing PR#1662.
* The methods package no longer directly copies slots (attributes)
into a prototype that is of an "abnormal" (reference) type, like
a symbol.
* The methods package no longer attempts to call length<-() on NULL
(during the bootstrap process).
* The methods package correctly shows methods when there are
multiple methods with the same signature for the same generic
(still not fully supported, but at least the user can see them).
* 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. (PR#17342)
* .C() when returning a logical vector now always maps values other
than FALSE and NA to TRUE (as documented).
* Subassignment with zero length vectors now coerces as documented
(PR#17344).
Further, x <- numeric(); x[1] <- character() now signals an error
'replacement has length zero' (or a translation of that) instead
of doing nothing.
* (Package parallel.) 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. (PR#17373)
* 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 PR#17280).
* The 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 PR#17369 and
PR#17381. The methods for matrices and arrays are changed
accordingly.
* Calling 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.
* Indexing a list using dollar and empty string (l$"") returns
NULL.
* Using \usage{ data(<name>, package="<pkg>") } no
longer produces
R CMD check warnings.
* match.arg() more carefully chooses the environment for
constructing default choices, fixing PR#17401 as proposed by
Duncan Murdoch.
* Deparsing of consecutive ! 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 PR#17397. (As a
side effect, this uses fewer parentheses in some other deparsing
involving ! calls.)
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
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