Version: 3.5.0-bp150.2.5
* Mon Apr 23 2018 detlef.steuer@gmx.de
- 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no longer valid (e.g. because some other process has cleaned up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.)
* Wed Mar 28 2018 darin@darins.net
- added gcc-c++ build dependency
* Tue Mar 20 2018 detlef.steuer@gmx.de
- Setting correctly R_UNZIPCMD
Corrects this bug: http://bugzilla.suse.com/show_bug.cgi?id=1083075
* Thu Mar 15 2018 detlef.steuer@gmx.de
- upstrem updated to 3.4.4
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 D'enes T'oth.
* 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)
* R CMD INSTALL now correctly sets C++ compiler flags when all
source files are in sub-directories of src.
* Mon Mar 12 2018 crrodriguez@opensuse.org
- Do not buildrequire xorg-x11-devel but individual x libs.
* Thu Nov 30 2017 detlef.steuer@gmx.de
- upstream updated to 3.4.3
CHANGES IN R 3.4.3:
INSTALLATION on a UNIX-ALIKE:
* A workaround has been added for the changes in location of
time-zone files in macOS 10.13 'High Sierra' and again in
10.13.1, so the default time zone is deduced correctly from the
system setting when R is configured with --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.)
* Fix calling of methods on S4 generics that dispatch on ... when
the call contains ....
* Following Unicode 'Corrigendum 9', the UTF-8 representations of
U+FFFE and U+FFFF are now regarded as valid by utf8ToInt().
* range(c(TRUE, NA), finite = TRUE) and similar no longer return
NA. (Reported by Lukas Stadler.)
* The self starting function 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.
* The printing of named raw vectors is now formatted nicely as for
other such atomic vectors, thanks to Lukas Stadler.
* Fri Sep 29 2017 detlef.steuer@gmx.de
- upstream update to 3.4.2
CHANGES IN R 3.4.2:
NEW FEATURES:
* Setting the 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).
* The version of LAPACK included in the sources has been updated to
3.7.1, a bug-fix release.
* The default for 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. (PR#17284)
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:
* The order of selection of OpenMP flags has been changed: Oracle
Developer Studio 12.5 accepts -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. (PR#17243)
* rt() assumed the ncp parameter was a scalar. (PR#17306)
* menu(choices) with more than 10 choices which easily fit into one
getOption("width")-line no longer erroneously repeats choices.
(PR#17312)
* length()<- on a pairlist succeeds. (<URL:
https://stat.ethz.ch/pipermail/r-devel/2017-July/074680.html>)
* Language objects such as quote(("\n")) or R functions are
correctly printed again, where R 3.4.1 accidentally duplicated
the backslashes.
* Construction of names() for very large objects in c() and
unlist() now works, thanks to Suharto Anggono's patch proposals
in PR#17292.
* Resource leaks (and similar) reported by Steve Grubb fixed.
(PR#17314, PR#17316, PR#17317, PR#17318, PR#17319, PR#17320)
* model.matrix(~1, mf) now gets the row names from mf also when
they differ from 1:nrow(mf), fixing PR#14992 thanks to the
suggestion by Sebastian Meyer.
* sigma(fm) now takes the correct denominator degrees of freedom
for a fitted model with NA coefficients. (PR#17313)
* 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 h in the latter case, and
hist.default(*, breaks) now checks and corrects a too large
breaks number. (PR#17274)
* 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).
* Setting options(device = *) to an invalid function no longer
segfaults when plotting is initiated. (PR#15883)
* encodeString(<very large string>) no longer segfaults.
(PR#15885)
* It is again possible to use configure --enable-maintainer-mode
without having installed notangle (it was required in R
3.4.[01]).
* S4 method dispatch on ... 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. (PR#17325)
* (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. (PR#17333)
* Running of finalizers after explicit GC request moved from the R
interface 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").
* The X11 device no longer uses the Xlib backing store (PR#16497).
* 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 PR#17333.
* splineDesign(.., derivs = 4) no longer segfaults.
* fisher.test(*, hybrid=TRUE) now (again) will use the hybrid
method when Cochran's conditions are met, fixing PR#16654.
* Thu Jul 27 2017 detlef.steuer@gmx.de
- Corrected "bug" "https://bugzilla.suse.com/show_bug.cgi?id=1049503
R now installs zip and unzip, what in turn eases the installation
of packages directly from github via devtools.
* Fri Jun 30 2017 detlef.steuer@gmx.de
- upstream update to 3.4.1
CHANGES IN R 3.4.1:
INSTALLATION on a UNIX-ALIKE:
* The deprecated support for PCRE versions older than 8.20 has been
removed.
BUG FIXES:
* getParseData() gave incorrect column information when code
contained multi-byte characters. (PR#17254)
* Asking for help using expressions like ?stats::cor() did not
work. (PR#17250)
* readRDS(url(....)) now works.
* R CMD Sweave again returns status = 0 on successful completion.
* Vignettes listed in .Rbuildignore were not being ignored
properly. (PR#17246)
* 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.
* (Windows only) The choose.files() function could return incorrect
results when called with multi = FALSE. (PR#17270)
* aggregate(<data.frame>, drop = FALSE) now also works in case of
near-equal numbers in by. (PR#16918)
* fourfoldplot() could encounter integer overflow when calculating
the odds ratio. (PR#17286)
* 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).
* Non-UTF-8 multibyte character sets were not handled properly in
source references. (PR#16732)
* Fri Apr 21 2017 detlef.steuer@gmx.de
- upstream update to 3.4.0
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.
* factor() now uses order() to sort its levels, not sort.list().
This makes factor() support custom vector-like objects if methods
for the appropriate generics are defined. This change 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.
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 PR#16527.
* 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
PR#16895.)
* 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 PR#17118.
* 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 PR#17116.
* 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 n <=
2500.
* 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 PR#16672.
* 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. (PR#16757)
* 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 SS1.6.4 of
'Writing R Extensions'.
Because it is needed by about 70 CRAN packages, headers R.h and
Rmath.h still declare
use namespace 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
using 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 SS5.4.1
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.
* An alternative compiler for C++11 is now specified with 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).
* There is a new macro 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.
* Support for the defunct IRIX and OSF/1 OSes and Alpha CPU has
been removed.
* 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.
* If available, the POSIX 2008 system call 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.)
* The minimum version requirement for 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:
* (Windows only) Tcl/Tk version 8.6.4 is now included in the binary
builds. The tcltk*.chm help file is no longer included; please
consult the online help at <URL: http://www.tcl.tk/man/> instead.
* The version of LAPACK included in the sources has been updated to
3.7.0: no new routines have been added to R.
PACKAGE INSTALLATION:
* There is support for compiling C++14 or C++17 code in packages on
suitable platforms: see 'Writing R Extensions' for how to request
this.
* The order of flags when 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).
* Packages which register native routines for .C or .Fortran need
to be re-installed for this version (unless installed with
R-devel SVN revision r72375 or later).
* Make variables with names containing 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).
* Tue Apr 18 2017 detlef.steuer@gmx.de
- And again that ldconfig call. Newline was obviously wrong.
Hopefully correct now.
* Tue Apr 04 2017 detlef.steuer@gmx.de
- Jan Engelhardt <jengelh@inai.de> asked for reverting the change
to the ldconfig call. So be it.
* Tue Mar 21 2017 detlef.steuer@gmx.de
- improvements for
a) calling /sbin/ldconfig, which no longer gives a warning
b) unregistering info-pages in %preun instead of %postun
* Tue Mar 07 2017 detlef.steuer@gmx.de
- a change in OBS now requires a BuildRequire: shadow for
some openSUSE releases.
* Mon Mar 06 2017 detlef.steuer@gmx.de
- upstream release 3.3.3
- Most important changes
CHANGES IN R 3.3.3:
NEW FEATURES:
* Changes when redirection of a http:// URL to a https:// URL is
encountered:
* The internal methods of download.file() and url() now report
that they cannot follow this (rather than failing silently).
* (Unix-alike) download.file(method = "auto") (the default)
re-tries with method = "libcurl".
* (Unix-alike) 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:
* The configure check for the zlib version is now robust to
versions longer than 5 characters, including 1.2.11.
UTILITIES:
* Environmental variable _R_CHECK_TESTS_NLINES_ controls how R CMD
check reports failing tests (see SS8 of the 'R Internals' manual).
DEPRECATED AND DEFUNCT:
* (C-level Native routine registration.) The undocumented styles
field of the components of R_CMethodDef and R_FortranMethodDef is
deprecated.
BUG FIXES:
* vapply(x, *) now works with long vectors x. (PR#17174)
* isS3method("is.na.data.frame") and similar are correct now.
(PR#17171)
* grepRaw(<long>, <short>, fixed = TRUE) now works, thanks to a
patch by Mikko Korpela. (PR#17132)
* Package installation into a library where the package exists
_via_ symbolic link now should work wherever Sys.readlink()
works, resolving PR#16725.
* "Cincinnati" was missing an "n" in the precip dataset.
* Fix buffer overflow vulnerability in 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 PR#17184.
* Sys.timezone() now returns non-NA also on platforms such as
Ubuntu 14.04.5 LTS, thanks to Mikko Korpela's PR#17186.
* format(x) for an illegal "POSIXlt" object x no longer segfaults.
* methods(f) now also works for f "(" or "{".
* (Windows only) dir.create() did not check the length of the path
to create, and so could overflow a buffer and crash R.
(PR#17206)
* On some systems, very small hexadecimal numbers in hex notation
would underflow to zero. (PR#17199)
* pmin() and pmax() now work again for ordered factors and 0-length
S3 classed objects, thanks to Suharto Anggono's PR#17195 and
PR#17200.
* 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.
* Bandwidth selectors 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 XR and
XRJulia on CRAN.)
* qbeta() underflowed too early in some very asymmetric cases.
(PR#17178)
* R CMD Rd2pdf had problems with packages with non-ASCII titles in
.Rd files (usually the titles were omitted).
* Mon Oct 31 2016 detlef.steuer@gmx.de
- upstream release 3.3.2
- Most important changes
CHANGES IN R 3.3.2:
NEW FEATURES:
* extSoftVersion() now reports the version (if any) of the readline
library in use.
* The version of LAPACK included in the sources has been updated to
3.6.1, a bug-fix release including a speedup for the
non-symmetric case of eigen().
* Use 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.
* The online documentation for package methods is extensively
rewritten. The goals are to simplify documentation for basic
use, to note old features not recommended and to correct
out-of-date information.
* Calls to 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:
* Versions of the 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). (PR#16604)
* 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:
* Use of the C/C++ macro 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:
* The check for non-portable flags in R CMD check could be stymied
by src/Makevars files which contained targets.
* (Windows only) When using certain desktop themes in Windows 7 or
higher, Alt-Tab could cause Rterm to stop accepting input.
(PR#14406; patch submitted by Jan Gleixner.)
* pretty(d, ..) behaves better for date-time d (PR#16923).
* When an S4 class name matches multiple classes in the S4 cache,
perform a dynamic search in order to obey namespace imports.
This should eliminate annoying messages about multiple hits in
the class cache. Also, pass along the package from the
ClassExtends object when looking up superclasses in the cache.
* sample(NA_real_) now works.
* Packages using non-ASCII encodings in their code did not install
data properly on systems using different encodings.
* merge(df1, df2) now also works for data frames with column names
"na.last", "decreasing", or "method". (PR#17119)
* 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.)
* (Windows only) R CMD SHLIB failed when a symbol in the resulting
library had the same name as a keyword in the .def file.
(PR#17130)
* pmax() and pmin() now work with (more ?) classed objects, such
as "Matrix" from the Matrix 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.)
* If a package added a class to a class union in another package,
loading the first package gave erroneous warnings about
"undefined subclass".
* 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.
(PR#17155)
* Using 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. (PR#17139)
* min() and max() now also work correctly when the argument list
starts with character(0). (PR#17160)
* Subsetting very large matrices (prod(dim(.)) >= 2^31) now works
thanks to Michael Schubmehl's PR#17158.
* 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 p in case of singularities (also for which = 5).
(PR#17161)
* xtabs(~ exclude) no longer fails from wrong scope, thanks to
Suharto Anggono's PR#17147.
* Reference class calls to 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.)
* Fri Jul 01 2016 toddrme2178@gmail.com
- Fix typo in Group tag.
* Tue Jun 21 2016 detlef.steuer@gmx.de
- upstream release 3.3.1
- Most important changes
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. (PR#16885.)
* 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 (PR#16923) and on 'inaccurate' platforms such as
32-bit windows or a configuration with --disable-long-double; see
comment #15 of PR#16761.
* In 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.
* Use of Ctrl-C to terminate a reverse incremental search started
by Ctrl-R in the readline-based Unix terminal interface is now
supported for readline >= 6.3 (Ctrl-G always worked). (PR#16603)
* diff(<difftime>) now keeps the "units" attribute, as subtraction
already did, PR#16940.
* Wed May 18 2016 detlef.steuer@gmx.de
- further cleanup of spec file.
Removed unneeded explicit Requires for
libcairo2/libfreetype6/liblzma5/libreadline6
Removed removal of backup file that was meanwhile removed upstream.
* Wed May 11 2016 detlef.steuer@gmx.de
- clean up of spec file after comments from Jan Engelhardt in
https://build.opensuse.org/request/show/393426
Some unneeded explicit BuildRequires removed.