R 3.5.0 is launched! (main launch with many new options)

R 3.5.0 (codename “Pleasure in Taking part in”) was launched yesterday. You will get the most recent binaries model from right here. (or the .tar.gz supply code from right here).

This can be a main launch with many new options and bug fixes, the complete checklist is supplied under.

Upgrading R on Home windows and Mac

In case you are utilizing Home windows you possibly can simply improve to the most recent model of R utilizing the installr bundle. Merely run the next code in Rgui:

set up.packages("installr") # set up 
setInternet2(TRUE) # just for R variations older than 3.3.0
installr::updateR() # updating R.
# If you want it to go quicker, run: installr::updateR(T)

Working “updateR()” will detect if there’s a new R model accessible, and in that case it can obtain+set up it (and many others.). There may be additionally a step-by-step tutorial (with screenshots) on how one can improve R on Home windows, utilizing the installr bundle. In case you solely see the choice to improve to an older model of R, then change your mirror or strive once more in a couple of hours (it often take round 24 hours for all CRAN mirrors to get the most recent model of R).

In case you are utilizing Mac you possibly can simply improve to the most recent model of R utilizing Andrea Cirillo’s updateR bundle. The bundle shouldn’t be on CRAN, so that you’ll have to run the next code in Rgui:

set up.packages("devtools")
devtools::install_github("AndreaCirilloAC/updateR")
updateR(admin_password = "PASSWORD") # The place "PASSWORD" stands to your system password

Later this 12 months Andrea and I intend to merge the updateR bundle into installr in order that the updateR perform will work seamlessly in each Home windows and Mac. Keep tuned 🙂

CHANGES IN R 3.5.0

SIGNIFICANT USER-VISIBLE CHANGES

All packages are by default byte-compiled on set up. This makes the put in packages bigger (often marginally so) and should have an effect on the format of messages and tracebacks (which regularly exclude .Name and comparable).

NEW FEATURES

issue() now makes use of order() to kind its ranges, quite than kind.checklist(). This enables issue() to assist customized vector-like objects if strategies for the suitable generics are outlined. It has the facet impact of constructing issue() succeed on empty or length-one non-atomic vector(-like) varieties (e.g., "checklist"), the place it failed earlier than.
diag() will get an optionally available names argument: this may occasionally require updates to packages defining S4 strategies for it.
chooseCRANmirror() and chooseBioCmirror() not have a useHTTPS argument, not wanted now all R builds assist https:// downloads.
New abstract() technique for warnings() with a (considerably experimental) print() technique.
(strategies bundle.) .self is now mechanically registered as a worldwide variable when registering a reference class technique.
tempdir(examine = TRUE) recreates the tempdir() listing whether it is not legitimate (e.g. as a result of another course of has cleaned up the ‘/tmp’ listing).
New askYesNo() perform and "askYesNo" choice to ask the consumer binary response questions in a customizable however constant manner. (Suggestion of PR#17242.)
New low stage utilities ...elt(n) and ...size() for working with ... elements inside a perform.
isTRUE() is extra tolerant and now true in
```
   x <- rlnorm(99)
   isTRUE(median(x) == quantile(x)["50%"])
```
New perform isFALSE() outlined analogously to isTRUE().
The default image desk dimension has been elevated from 4119 to 49157; this may occasionally enhance the efficiency of image decision when many packages are loaded. (Recommended by Jim Hester.)
line() will get a brand new possibility iter = 1.
Studying from connections in textual content mode is buffered, considerably bettering the efficiency of readLines(), in addition to scan() and learn.desk(), not less than when specifying colClasses.
order() is smarter about choosing a default kind technique when its arguments are objects.
accessible.packages() has two new arguments which management if the values from the per-session repository cache are used (default true, as earlier than) and in that case how previous cached values could be for use (default one hour).These arguments could be handed from set up.packages(), replace.packages() and capabilities calling that: to allow this accessible.packages(), packageStatus() andobtain.file() acquire a ... argument.
packageStatus()‘s improve() technique not ignores its ... argument however passes it to set up.packages().
put in.packages() beneficial properties a ... argument to permit arguments (together with noCache) to be handed from new.packages(), previous.packages(), replace.packages() and packageStatus().
issue(x, ranges, labels) now permits duplicated labels (not duplicated ranges!). Therefore you possibly can map totally different values of x to the identical stage straight.
Making an attempt to make use of names<-() on an S4 spinoff of a primary kind not emits a warning.
The checklist technique of inside() beneficial properties an possibility keepAttrs = FALSE for some speed-up.
system() and system2() now enable the specification of a most elapsed time (‘timeout’).
debug() helps debugging of strategies on any object of S4 class "genericFunction", together with group generics.
Making an attempt to extend the size of a variable containing NULL utilizing size()<- nonetheless has no impact on the goal variable, however now triggers a warning.
kind.convert() turns into a generic perform, with extra strategies that function recursively over checklist and knowledge.body objects. Courtesy of Arni Magnusson (PR#17269).
decrease.tri(x) and higher.tri(x) solely needing dim(x) now work through new capabilities .row() and .col(), so not name as.matrix() by default in an effort to work effectively for all type of matrix-like objects.
print() strategies for "xgettext" and "xngettext" now use encodeString() which retains, e.g. "n", seen. (Want of PR#17298.)
bundle.skeleton() beneficial properties an optionally available encoding argument.
approx(), spline(), splinefun() and approxfun() additionally work for lengthy vectors.
deparse() and dump() are extra helpful for S4 objects, dput() now utilizing the identical inner C code as an alternative of its earlier imperfect workaround R code. S4 objects now usually deparse completely, i.e., could be recreated identically from deparsed code.dput(), deparse() and dump() now print the names() info solely as soon as, utilizing the extra readable (tag = worth) syntax, notably for checklist()s, i.e., together with knowledge frames.
These capabilities acquire a brand new management possibility "niceNames" (see .deparseOpts()), which when set (as by default) additionally makes use of the (tag = worth) syntax for atomic vectors. However, with out deparse choices "showAttributes" and "niceNames", names are not proven additionally for lists. as.character(checklist( c (one = 1))) now contains the title, as as.character(checklist(checklist(one = 1))) has all the time carried out.

m:n now additionally deparses properly when m > n.

The "quoteExpressions" possibility, additionally a part of "all", not quote()s formulation as that won’t re-parse identically. (PR#17378)
If the choice setWidthOnResize is about and TRUE, R run in a terminal utilizing a current readline library will set the width possibility when the terminal is resized. Recommended by Ralf Goertz.
If a number of on.exit() expressions are set utilizing add = TRUE then all expressions will now be run even when one indicators an error.
mclapply() will get an possibility affinity.checklist which permits extra environment friendly execution with heterogeneous processors, because of Helena Kotthaus.
The character strategies for as.Date() and as.POSIXlt() are extra versatile through new arguments tryFormats and optionally available: see their assist pages.
on.exit() beneficial properties an optionally available argument after with default TRUE. Utilizing after = FALSE with add = TRUE provides an exit expression earlier than any current ones. This manner the expressions are run in a first-in last-out style. (From Lionel Henry.)
On Home windows, file.rename() internally retries the operation in case of error to aim to recuperate from potential anti-virus interference.
Command line completion on :: now additionally contains lazy-loaded knowledge.
If the TZ setting variable is about when date-time capabilities are first used, it’s recorded because the session default and so can be used quite than the default deduced from the OS if TZ is subsequently unset.
There may be 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 = ), 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) 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 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’ §C.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 usingSET_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 + µI 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() 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(, 3) now works, thanks to prompting by Marc Schwartz.
readLines() no longer segfaults on very large files with embedded '' (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 = ) 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 = " 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 indicators an error ‘alternative has size zero’ (or a translation of that) as an alternative of doing nothing.
(Bundle parallel.) mclapply(), pvec() and mcparallel() (when mccollect() is used to gather outcomes) not depart zombie processes behind.
R CMD INSTALL now produces the meant error message when, e.g., the LazyData subject is invalid.
as.matrix(dd) now works when the information body dd incorporates a column which is a knowledge body or matrix, together with a 0-column matrix/d.f. .
mclapply(X, mc.cores) now follows its documentation and calls lapply() in case mc.cores = 1 additionally within the case mc.preschedule is fake. (PR#17373)
mixture(, drop=FALSE) not calls the perform on elements however units corresponding outcomes to NA. (Because of Suharto Anggono’s patches in PR#17280).
The duplicated() technique for knowledge frames is now primarily based on the checklist technique (as an alternative of string coercion). Consequently distinctive() is best distinguishing knowledge body rows, fixing PR#17369 and PR#17381. The strategies for matrices and arrays are modified accordingly.
Calling names() on an S4 object derived from "setting" behaves (by default) like calling names() on an strange setting.
learn.desk() with a non-default separator now helps quotes following a non-whitespace character, matching the conduct of scan().
parLapplyLB and parSapplyLB have been fastened to do load balancing (dynamic scheduling). This additionally signifies that outcomes of computations relying on random quantity turbines will now actually be non-reproducible, as documented.
Indexing an inventory utilizing greenback and empty string (l$"") returns NULL.
Utilizing utilization{ knowledge(, bundle="") } not produces R CMD examine warnings.
match.arg() extra rigorously chooses the setting for establishing default decisions, fixing PR#17401 as proposed by Duncan Murdoch.
Deparsing of consecutive ! calls is now according to deparsing unary - and + calls and creates code that may be reparsed precisely; because of a patch by Lionel Henry inPR#17397. (As a facet impact, this makes use of fewer parentheses in another deparsing involving ! calls.)

R 3.5.0 is launched! (main launch with many new options)

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