Log Message:
Update to 3.5.0

Upstream changes:
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tempdir(check = TRUE) recreates the tempdir() directory if it is no longer valid \ 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 \ 
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 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 + 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(<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.)

[R logo] 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.

The version of LAPACK included in the sources has been updated to 3.8.0 (for the \ 
routines used by R, a very minor bug-fix change).

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).

Legacy support of 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. (PR#17345)

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 PR#17367)

R CMD build checks for GNU cp rather than assuming Linux has it. (PR#17370 says \ 
‘Alpine Linux’ does not.)

Non-UTF-8 multibyte character handling fixed more permanently (PR#16732).

sum(<large ints>, <stuff>) is more consistent. (PR#17372)

rf() and rbeta() now also work correctly when ncp is not scalar, notably when \ 
(partly) NA. (PR#17375)

is.na(NULL) no longer warns. (PR#16107)

R CMD INSTALL now correctly sets C++ compiler flags when all source files are in \ 
sub-directories of ‘src’.