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no longer valid (e.g. because some other process has cleaned up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.
Version: 3.2.5-5.1
* Fri Apr 15 2016 detlef.steuer@gmx.de
- CHANGES IN R 3.2.5:
BUG FIXES:
? format.POSIXlt() behaved incorrectly in R 3.2.4. E.g. the output
of format(as.POSIXlt(paste0(1940:2000,"-01-01"), tz = "CET"),
usetz = TRUE) ended in two "CEST" time formats.
? A typo in the Makefile for src/extra/xz prevented builds of
liblzma.a. (Notice that this will become unbundled in 3.3.0.)
* Thu Mar 17 2016 detlef.steuer@gmx.de
- upstrem releases minorst bug fix release
NEWS: The 3.2.4 release had two annoyances which we would rather
not have in an "ultra-stable" release, designed to hang around
for the duration of the 3.3 series. One was a relatively minor
Makefile issue affecting system using R's bundled lzma library.
The other, rather more serious, affected printing and formatting
of POSIXlt objects, which would unpredictably get the Daylight
Savings Time wrong.
* Fri Mar 11 2016 detlef.steuer@gmx.de
- Some version numbers of recommended packages corrected
* Fri Mar 11 2016 detlef.steuer@gmx.de
- Release numbers for sub-packages improved
* Fri Mar 11 2016 detlef.steuer@gmx.de
- added MakefileTypo.patch to enable building for 12.2
was a one charcter show stopper
* Thu Mar 10 2016 detlef.steuer@gmx.de
- upstream release 3.2.4, only minor improvements
CHANGES IN R 3.2.4:
NEW FEATURES:
? install.packages() and related functions now give a more
informative warning when an attempt is made to install a base
package.
? summary(x) now prints with less rounding when x contains infinite
values. (Request of PR#16620.)
? provideDimnames() gets an optional unique argument.
? shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows.
(Response to PR#16636.)
? The data.frame method of rbind() gains an optional argument
stringsAsFactors (instead of only depending on
getOption("stringsAsFactors")).
? smooth(x, *) now also works for long vectors.
? tools::texi2dvi() has a workaround for problems with the texi2dvi
script supplied by texinfo 6.1.
It extracts more error messages from the LaTeX logs when in
emulation mode.
UTILITIES:
? R CMD check will leave a log file build_vignettes.log from the
re-building of vignettes in the .Rcheck directory if there is a
problem, and always if environment variable
_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set to a true value.
DEPRECATED AND DEFUNCT:
? Use of SUPPORT_OPENMP from header Rconfig.h is deprecated in
favour of the standard OpenMP define _OPENMP.
(This has been the recommendation in the manual for a while now.)
? The make macro AWK which is long unused by R itself but recorded
in file etc/Makeconf is deprecated and will be removed in R
3.3.0.
? The C header file S.h is no longer documented: its use should be
replaced by R.h.
* Mon Mar 07 2016 detlef.steuer@gmx.de
- The big split up. What was a monolithic R-base*rpm now is
divided over 30 something packages, with the following layout.
R-base-3.2.3: dummy packages, contains all of R
Use R-base, if you don´t have a good understandig what it means
to install only parts of it!
R-base-devel-3.2.3: dummy, contains R-core-devel
R-core-3.2.3: R core, no packages at all
R-core-devel-3.2.3: devel files
R-core-libs-3.2.3: contains Rlib
R-core-doc-3.2.3: all the documentation of R-core
R-core-packages-3.2.3: dummy package to load all core packages, that are
R-compiler-3.2.3,
R-datasets-3.2.3,
R-grDevices-3.2.3,
R-graphics-3.2.3,
R-grid-3.2.3,
R-methods-3.2.3,
R-parallel-3.2.3,
R-splines-3.2.3,
R-stats-3.2.3,
R-stats4-3.2.3,
R-tcltk-3.2.3,
R-tools-3.2.3,
R-utils-3.2.3.
Each of these packages may be installed alone.
R-recommended-packages-3.2.3: dummy package to load all recommeded
packages, that are
R-boot-1.3.17,
R-class-7.3.14,
R-cluster-2.0.3,
R-codetools-0.2.14,
R-foreign-0.8.66,
R-KernSmooth-2.23.15,
R-lattice-0.20.33,
R-MASS-7.3.45,
R-Matrix-1.2.3, R-Matrix-devel-1.2.3,
R-mgcv-1.8.9,
R-nlme-3.1.122,
R-nnet-7.3.11,
R-rpart-4.1.10,
R-spatial-7.3.11,
R-survival-2.38.3.
Each of these packages may be installed alone.
* Fri Dec 11 2015 detlef.steuer@gmx.de
- Upstream release R-3.2.3
CHANGES IN R 3.2.3:
NEW FEATURES:
* Some recently-added Windows time zone names have been added to
the conversion table used to convert these to Olson names.
(Including those relating to changes for Russia in Oct 2014, as
in PR#16503.)
* (Windows) Compatibility information has been added to the
manifests for Rgui.exe, Rterm.exe and Rscript.exe. This should
allow win.version() and Sys.info() to report the actual Windows
version up to Windows 10.
* Windows "wininet" FTP first tries EPSV / PASV mode rather than
only using active mode (reported by Dan Tenenbaum).
* which.min(x) and which.max(x) may be much faster for logical and
integer x and now also work for long vectors.
* The 'emulation' part of tools::texi2dvi() has been somewhat
enhanced, including supporting quiet = TRUE. It can be selected
by texi2dvi = "emulation".
(Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015:
tools::texi2dvi() tries texify.exe if it is not found.
* (Windows only) Shortcuts for printing and saving have been added
to menus in Rgui.exe. (Request of PR#16572.)
* loess(..., iterTrace=TRUE) now provides diagnostics for
robustness iterations, and the print() method for
summary(<loess>) shows slightly more.
* The included version of PCRE has been updated to 8.38, a bug-fix
release.
* View() now displays nested data frames in a more friendly way.
(Request with patch in PR#15915.)
INSTALLATION and INCLUDED SOFTWARE:
* The included configuration code for libintl has been updated to
that from gettext version 0.19.5.1 - this should only affect how
an external library is detected (and the only known instance is
under OpenBSD). (Wish of PR#16464.)
* configure has a new argument --disable-java to disable the checks
for Java.
* The configure default for MAIN_LDFLAGS has been changed for the
FreeBSD, NetBSD and Hurd OSes to one more likely to work with
compilers other than gcc (FreeBSD 10 defaults to clang).
* configure now supports the OpenMP flags -fopenmp=libomp (clang)
and -qopenmp (Intel C).
* Various macros can be set to override the default behaviour of
configure when detecting OpenMP: see file config.site.
* Source installation on Windows has been modified to allow for
MiKTeX installations without texi2dvi.exe. See file
MkRules.dist.
BUG FIXES:
* regexpr(pat, x, perl = TRUE) with Python-style named capture did
not work correctly when x contained NA strings. (PR#16484)
* The description of dataset ToothGrowth has been
improved/corrected. (PR#15953)
* model.tables(type = "means") and hence TukeyHSD() now support
"aov" fits without an intercept term. (PR#16437)
* close() now reports the status of a pipe() connection opened with
an explicit open argument. (PR#16481)
* Coercing a list without names to a data frame is faster if the
elements are very long. (PR#16467)
* (Unix-only) Under some rare circumstances piping the output from
Rscript or R -f could result in attempting to close the input
file twice, possibly crashing the process. (PR#16500)
* (Windows) Sys.info() was out of step with win.version() and did
not report Windows 8.
* topenv(baseenv()) returns baseenv() again as in R 3.1.0 and
earlier. This also fixes compilerJIT(3) when used in .Rprofile.
* detach()ing the methods package keeps .isMethodsDispatchOn()
true, as long as the methods namespace is not unloaded.
* Removed some spurious warnings from configure about the
preprocessor not finding header files. (PR#15989)
* rchisq(*, df=0, ncp=0) now returns 0 instead of NaN, and
dchisq(*, df=0, ncp=*) also no longer returns NaN in limit cases
(where the limit is unique). (PR#16521)
* pchisq(*, df=0, ncp > 0, log.p=TRUE) no longer underflows (for
ncp > ~60).
* nchar(x, "w") returned -1 for characters it did not know about
(e.g. zero-width spaces): it now assumes 1. It now knows about
most zero-width characters and a few more double-width
characters.
* Help for which.min() is now more precise about behavior with
logical arguments. (PR#16532)
* The print width of character strings marked as "latin1" or
"bytes" was in some cases computed incorrectly.
* abbreviate() did not give names to the return value if minlength
was zero, unlike when it was positive.
* (Windows only) dir.create() did not always warn when it failed to
create a directory. (PR#16537)
* When operating in a non-UTF-8 multibyte locale (e.g. an East
Asian locale on Windows), grep() and related functions did not
handle UTF-8 strings properly. (PR#16264)
* read.dcf() sometimes misread lines longer than 8191 characters.
(Reported by Herv'e Pag`es with a patch.)
* within(df, ..) no longer drops columns whose name start with a
".".
* The built-in HTTP server converted entire Content-Type to
lowercase including parameters which can cause issues for
multi-part form boundaries (PR#16541).
* Modifying slots of S4 objects could fail when the methods package
was not attached. (PR#16545)
* splineDesign(*, outer.ok=TRUE) (splines) is better now
(PR#16549), and interpSpline() now allows sparse=TRUE for speedup
with non-small sizes.
* If the expression in the traceback was too long, traceback() did
not report the source line number. (Patch by Kirill M"uller.)
* The browser did not truncate the display of the function when
exiting with options("deparse.max.lines") set. (PR#16581)
* When bs(*, Boundary.knots=) had boundary knots inside the data
range, extrapolation was somewhat off. (Patch by Trevor Hastie.)
* var() and hence sd() warn about factor arguments which are
deprecated now. (PR#16564)
* loess(*, weights = *) stored wrong weights and hence gave
slightly wrong predictions for newdata. (PR#16587)
* aperm(a, *) now preserves names(dim(a)).
* poly(x, ..) now works when either raw=TRUE or coef is specified.
(PR#16597)
* data(package=*) is more careful in determining the path.
* prettyNum(*, decimal.mark, big.mark): fixed bug introduced when
fixing PR#16411.
* Thu Dec 10 2015 detlef.steuer@gmx.de
- Reverse the whole split. Back to the big package.
Had user reports of broken installations.
R-base, R-base-devel and R-base-libs are provided for now.
The big split will come for 3.3.0
* Wed Dec 09 2015 detlef.steuer@gmx.de
- R-base was changed from a giant monolith to thirty-some packages.
There were requests to use the libs without the interpreter.
Furthermore it is now possible to use a frugal installation of R.
The following binaries are built now:
R-base-3.2.2-5.1.x86_64.rpm : A Meta-package. Use this, and it looks
just like it looked the last 10 years.
Requires base and recommended packages.
R-base-devel-3.2.2-5.1.x86_64.rpm: Just for backward compatibility.
R-core-3.2.2-5.1.x86_64.rpm
R-core-libs-3.2.2-5.1.x86_64.rpm
R-core-devel-3.2.2-5.1.x86_64.rpm : The R-core packages install
a bare-bones R. No packages inculded.
R-grid-3.2.2-5.1.x86_64.rpm
R-graphics-3.2.2-5.1.x86_64.rpm
R-grDevices-3.2.2-5.1.x86_64.rpm
R-datasets-3.2.2-5.1.x86_64.rpm
R-stats4-3.2.2-5.1.x86_64.rpm
R-methods-3.2.2-5.1.x86_64.rpm
R-tcltk-3.2.2-5.1.x86_64.rpm
R-compiler-3.2.2-5.1.x86_64.rpm
R-parallel-3.2.2-5.1.x86_64.rpm
R-splines-3.2.2-5.1.x86_64.rpm
R-stats-3.2.2-5.1.x86_64.rpm
R-utils-3.2.2-5.1.x86_64.rpm
R-tools-3.2.2-5.1.x86_64.rpm : All the base packages.
R-recommended-3.2.2-5.1.x86_64.rpm : A meta-package including all
recommended packages.
R-cluster-2.0.3-5.1.x86_64.rpm
R-nlme-3.1.121-5.1.x86_64.rpm
R-lattice-0.20.33-5.1.x86_64.rpm
R-class-7.3.13-5.1.x86_64.rpm
R-Matrix-devel-1.2.2-5.1.x86_64.rpm
R-codetools-0.2.14-5.1.x86_64.rpm
R-survival-2.38.3-5.1.x86_64.rpm
R-rpart-4.1.10-5.1.x86_64.rpm
R-MASS-7.3.43-5.1.x86_64.rpm
R-mgcv-1.8.7-5.1.x86_64.rpm
R-foreign-0.8.65-5.1.x86_64.rpm
R-nnet-7.3.10-5.1.x86_64.rpm
R-Matrix-1.2.2-5.1.x86_64.rpm
R-boot-1.3.17-5.1.x86_64.rpm
R-KernSmooth-2.23.15-5.1.x86_64.rpm
R-spatial-7.3.10-5.1.x86_64.rpm : All recommended packaged.
Note: They now have their own version
numbers, so it should be much easier to
use newer Versions of the recommended
packages.
And the source RPM for all the above.
R-base-3.2.2-5.1.src.rpm
* Wed Aug 19 2015 badshah400@gmail.com
- Disable building man files for openSUSE:42.
* Mon Aug 17 2015 detlef.steuer@gmx.de
- Upstream release 3.2.2
- Most important
CHANGES IN R 3.2.2:
SIGNIFICANT USER-VISIBLE CHANGES:
* It is now easier to use secure downloads from https:// URLs on
builds which support them: no longer do non-default options need
to be selected to do so. In particular, packages can be
installed from repositories which offer https:// URLs, and those
listed by setRepositories() now do so (for some of their
mirrors).
Support for https:// URLs is available on Windows, and on other
platforms if support for libcurl was compiled in and if that
supports the https protocol (system installations can be expected
to do). So https:// support can be expected except on rather old
OSes (an example being OS X 'Snow Leopard', where a non-system
version of libcurl can be used).
(Windows only) The default method for accessing URLs _via_
download.file() and url() has been changed to be "wininet" using
Windows API calls. This changes the way proxies need to be set
and security settings made: there have been some reports of sites
being inaccessible under the new default method (but the previous
methods remain available).
NEW FEATURES:
* cmdscale() gets new option list. for increased flexibility when a
list should be returned.
* configure now supports texinfo version 6.0, which (unlike the
change from 4.x to 5.0) is a minor update. (Wish of PR#16456.)
* (Non-Windows only) download.file() with default method = "auto"
now chooses "libcurl" if that is available and a https:// or
ftps:// URL is used.
* (Windows only) setInternet2(TRUE) is now the default. The
command-line option --internet2 and environment variable
R_WIN_INTERNET2 are now ignored.
Thus by default the "internal" method for download.file() and
url() uses the "wininet" method: to revert to the previous
default use setInternet2(FALSE).
This means that https:// can be read by default by
download.file() (they have been readable by file() and url()
since R 3.2.0).
There are implications for how proxies need to be set (see
?download.file): also, cacheOK = FALSE is not supported.
* chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
in preference to HTTP mirrors. This changes the interpretation
of their ind arguments: see their help pages.
* capture.output() gets optional arguments type and split to pass
to sink(), and hence can be used to capture messages.
C-LEVEL FACILITIES:
* Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
the alloca.h header (it is needed to define alloca on Solaris and
AIX, at least: see 'Writing R Extensions' for how to use it).
INSTALLATION and INCLUDED SOFTWARE:
* The libtool script generated by configure has been modified to
support FreeBSD >= 10 (PR#16410).
BUG FIXES:
* The HTML help page links to demo code failed due to a change in R
3.2.0. (PR#16432)
* If the na.action argument was used in model.frame(), the original
data could be modified. (PR#16436)
* getGraphicsEvent() could cause a crash if a graphics window was
closed while it was in use. (PR#16438)
* matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
"expression".
* strptime() could overflow the allocated storage on the C stack
when the timezone had a non-standard format much longer than the
standard formats. (Part of PR#16328.)
* options(OutDec = s) now signals a warning (which will become an
error in the future) when s is not a string with exactly one
character, as that has been a documented requirement.
* prettyNum() gains a new option input.d.mark which together with
other changes, e.g., the default for decimal.mark, fixes some
format()ting variants with non-default getOption("OutDec") such
as in PR#16411.
* download.packages() failed for type equal to either "both" or
"binary". (Reported by Dan Tenenbaum.)
* The dendrogram method of labels() is much more efficient for
large dendrograms, now using rapply(). (Comment #15 of PR#15215)
* The "port" algorithm of nls() could give spurious errors.
(Reported by Radford Neal.)
* Reference classes that inherited from reference classes in
another package could invalidate methods of the inherited class.
Fixing this requires adding the ability for methods to be
"external", with the object supplied explicitly as the first
argument, named .self. See "Inter-Package Superclasses" in the
documentation.
* readBin() could fail on the SPARC architecture due to alignment
issues. (Reported by Radford Neal.)
* qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
of returning NaN. (PR#16475)
* Auto-printing of S3 and S4 values now searches for print() in the
base namespace and show() in the methods namespace instead of
searching the global environment.
* polym() gains a coefs = NULL argument and returns class "poly"
just like poly() which gets a new simple=FALSE option. They now
lead to correct predict()ions, e.g., on subsets of the original
data.
* rhyper(nn, <large>) now works correctly. (PR#16489)
* ttkimage() did not (and could not) work so was removed. Ditto for
tkimage.cget() and tkimage.configure(). Added two Ttk widgets and
missing subcommands for Tk's image command: ttkscale(),
ttkspinbox(), tkimage.delete(), tkimage.height(),
tkimage.inuse(), tkimage.type(), tkimage.types(),
tkimage.width(). (PR#15372, PR#16450)
* getClass("foo") now also returns a class definition when it is
found in the cache more than once.
* Thu Jun 18 2015 detlef.steuer@gmx.de
- Upstream release 3.2.1
- Improvement of build: include libcurl and texlive-dvips/
texlive-hevetic
- Most important
CHANGES IN R 3.2.1:
NEW FEATURES:
* utf8ToInt() now checks that its input is valid UTF-8 and returns
NA if it is not.
* install.packages() now allows type = "both" with repos = NULL if
it can infer the type of file.
* nchar(x, *) and nzchar(x) gain a new argument keepNA which
governs how the result for NAs in x is determined. For the R
3.2.x series, the default remains FALSE which is fully back
compatible. From R 3.3.0, the default will change to keepNA = NA
and you are advised to consider this for code portability.
* news() more flexibly extracts dates from package NEWS.Rd files.
* lengths(x) now also works (trivially) for atomic x and hence can
be used more generally as an efficient replacement of sapply(x,
length) and similar.
* The included version of PCRE has been updated to 8.37, a bug-fix
release.
* diag() no longer duplicates a matrix when extracting its
diagonal.
* as.character.srcref() gains an argument to allow characters
corresponding to a range of source references to be extracted.
BUG FIXES:
* acf() and ccf() now guarantee values strictly in [-1,1] (instead
of sometimes very slightly outside). PR#15832.
* as.integer("111111111111") now gives NA (with a warning) as it
does for the corresponding numeric or negative number coercions.
Further, as.integer(M + 0.1) now gives M (instead of NA) when M
is the maximal representable integer.
* On some platforms nchar(x, "c") and nchar(x, "w") would return
values (possibly NA) for inputs which were declared to be UTF-8
but were not, or for invalid strings without a marked encoding in
a multi-byte locale, rather than give an error. Additional
checks have been added to mitigate this.
* apply(a, M, function(u) c(X = ., Y = .)) again has dimnames
containing "X" and "Y" (as in R < 3.2.0).
* (Windows only) In some cases, the --clean option to R CMD INSTALL
could fail. (PR#16178)
* (Windows only) choose.files() would occasionally include
characters from the result of an earlier call in the result of a
later one. (PR#16270)
* A change in RSiteSearch() in R 3.2.0 caused it to submit invalid
URLs. (PR#16329)
* Rscript and command line R silently ignored incomplete statements
at the end of a script; now they are reported as parse errors.
(PR#16350)
* Parse data for very long strings was not stored. (PR#16354)
* plotNode(), the workhorse of the plot method for "dendrogram"s is
no longer recursive, thanks to Suharto Anggono, and hence also
works for deeply nested dendrograms. (PR#15215)
* The parser could overflow internally when given numbers in
scientific format with extremely large exponents. (PR#16358)
* If the CRAN mirror was not set, install.packages(type = "both")
and related functions could repeatedly query the user for it.
(Part of PR#16362)
* The low-level functions .rowSums() etc. did not check the length
of their argument, so could segfault. (PR#16367)
* The quietly argument of library() is now correctly propagated
from .getRequiredPackages2().
* Under some circumstances using the internal PCRE when building R
fron source would cause external libs such as -llzma to be
omitted from the main link.
* The .Primitive default methods of the logic operators, i.e., !, &
and |, now give correct error messages when appropriate, e.g.,
for `&`(TRUE) or `!`(). (PR#16385)
* cummax(x) now correctly propagates NAs also when x is of type
integer and begins with an NA.
* summaryRprof() could fail when the profile contained only two
records. (PR#16395)
* HTML vignettes opened using vignette() did not support links into
the rest of the HTML help system. (Links worked properly when
the vignette was opened using browseVignettes() or from within
the help system.)
* arima(*, xreg = .) (for d >= 1) computes estimated variances
based on a the number of effective observations as in R version
3.0.1 and earlier. (PR#16278)
* slotNames(.) is now correct for "signature" objects (mostly used
internally in methods).
* On some systems, the first string comparison after a locale
change would result in NA.
* Thu Apr 16 2015 detlef.steuer@gmx.de
- Upstream release 3.2.0
- Most important
CHANGES IN 3.2.0:
NEW FEATURES:
* anyNA() gains a recursive argument.
* When x is missing and names is not false (including the default
value), Sys.getenv(x, names) returns an object of class "Dlist"
and hence prints tidily.
* (Windows.) shell() no longer consults the environment variable
SHELL: too many systems have been encountered where it was set
incorrectly (usually to a path where software was compiled, not
where it was installed). R_SHELL, the preferred way to select a
non-default shell, can be used instead.
* Some unusual arguments to embedFonts() can now be specified as
character vectors, and the defaults have been changed
accordingly.
* Functions in the Summary group duplicate less. (PR#15798)
* (Unix-alikes.) system(cmd, input = ) now uses
'shell-execution-environment' redirection, which will be more
natural if cmd is not a single command (but requires a
POSIX-compliant shell). (Wish of PR#15508)
* read.fwf() and read.DIF() gain a fileEncoding argument, for
convenience.
* Graphics devices can add attributes to their description in
.Device and .Devices. Several of those included with R use a
"filepath" attribute.
* pmatch() uses hashing in more cases and so is faster at the
expense of using more memory. (PR#15697)
* pairs() gains new arguments to select sets of variables to be
plotted against each other.
* file.info(, extra_cols = FALSE) allows a minimal set of columns
to be computed on Unix-alikes: on some systems without
properly-configured caching this can be significantly faster with
large file lists.
* New function dir.exists() in package base to test efficiently
whether one or more paths exist and are directories.
* dput() and friends gain new controls hexNumeric and digits17
which output double and complex quantities as, respectively,
binary fractions (exactly, see sprintf("%a")) and as decimals
with up to 17 significant digits.
* save(), saveRDS() and serialize() now support ascii = NA which
writes ASCII files using sprintf("%a") for double/complex
quantities. This is read-compatible with ascii = TRUE but avoids
binary->decimal->binary conversions with potential loss of
precision. Unfortunately the Windows C runtime's lack of C99
compliance means that the format cannot be read correctly there
in R before 3.1.2.
* The default for formatC(decimal.mark =) has been changed to be
getOption("OutDec"); this makes it more consistent with format()
and suitable for use in print methods, e.g. those for classes
"density", "ecdf", "stepfun" and "summary.lm".
getOption("OutDec") is now consulted by the print method for
class "kmeans", by cut(), dendrogram(), plot.ts() and quantile()
when constructing labels and for the report from legend(trace =
TRUE).
(In part, wish of PR#15819.)
* printNum() and hence format() and formatC() give a warning if
big.mark and decimal.mark are set to the same value (period and
comma are not uncommonly used for each, and this is a check that
conventions have not got mixed).
* merge() can create a result which uses long vectors on 64-bit
platforms.
* dget() gains a new argument keep.source which defaults to FALSE
for speed (dput() and dget() are most often used for data objects
where this can make dget() many times faster).
* Packages may now use a file of common macro definitions in their
help files, and may import definitions from other packages.
* A number of macros have been added in the new share/Rd directory
for use in package overview help pages, and promptPackage() now
makes use of them.
* tools::parse_Rd() gains a new permissive argument which converts
unrecognized macros into text. This is used by
utils:::format.bibentry to allow LaTeX markup to be ignored.
* options(OutDec =) can now specify a multi-byte character, e.g.,
options(OutDec = "\u00b7") in a UTF-8 locale.
* is.recursive(x) is no longer true when x is an external pointer,
a weak reference or byte code; the first enables all.equal(x, x)
when x <- getClass(.).
* ls() (aka objects()) and as.list.environment() gain a new
argument sorted.
* The "source" attribute (which has not been added to functions by
R since before R version 2.14.0) is no longer treated as special.
* Function returnValue() has been added to give on.exit() code
access to a function's return value for debugging purposes.
* crossprod(x, y) allows more matrix coercions when x or y are
vectors, now equalling t(x) %*% y in these cases (also reported
by Radford Neal). Similarly, tcrossprod(x,y) and %*% work in
more cases with vector arguments.
* Utility function dynGet() useful for detecting cycles, aka
infinite recursions.
* The byte-code compiler and interpreter include new instructions
that allow many scalar subsetting and assignment and scalar
arithmetic operations to be handled more efficiently. This can
result in significant performance improvements in scalar
numerical code.
* apply(m, 2, identity) is now the same as the matrix m when it has
_named_ row names.
* A new function debuggingState() has been added, allowing to
temporarily turn off debugging.
* example() gets a new optional argument run.donttest and
tools::Rd2ex() a corresponding commentDonttest, with a default
such that example(..) in help examples will run \donttest code
only if used interactively (a change in behaviour).
* rbind.data.frame() gains an optional argument make.row.names, for
potential speedup.
* New function extSoftVersion() to report on the versions of
third-party software in use in this session. Currently reports
versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and
the iconv implementation.
A similar function grSoftVersion() in package grDevices reports
on third-party graphics software.
Function tcltk::tclVersion() reports the Tcl/Tk version.
* Calling callGeneric() without arguments now works with primitive
generics to some extent.
* vapply(x, FUN, FUN.VALUE) is more efficient notably for large
length(FUN.VALUE); as extension of PR#16061.
* as.table() now allows tables with one or more dimensions of
length 0 (such as as.table(integer())).
* names(x) <- NULL now clears the names of call and ... objects.
* library() will report a warning when an insufficient dependency
version is masking a sufficient one later on the library search
path.
* A new plot() method for class "raster" has been added.
* New check_packages_in_dir_changes() function in package tools for
conveniently analyzing how changing sources impacts the check
results of their reverse dependencies.
* Speed-up from Peter Haverty for ls() and
methods:::.requirePackage() speeding up package loading.
(PR#16133)
* New get0() function, combining exists() and get() in one call,
for efficiency.
* match.call() gains an envir argument for specifying the
environment from which to retrieve the ... in the call, if any;
this environment was wrong (or at least undesirable) when the
definition argument was a function.
* topenv() has been made .Internal() for speedup, based on Peter
Haverty's proposal in PR#16140.
* getOption() no longer calls options() in the main case.
* Optional use of libcurl (version 7.28.0 from Oct 2012 or later)
for Internet access:
* capabilities("libcurl") reports if this is available.
* libcurlVersion() reports the version in use, and other
details of the "libcurl" build including which URL schemes it
supports.
* curlGetHeaders() retrieves the headers for http://, https://,
ftp:// and ftps:// URLs: analysis of these headers can
provide insights into the `existence' of a URL (it might for
example be permanently redirected) and is so used in R CMD
check --as-cran.
* download.file() has a new optional method "libcurl" which
will handle more URL schemes, follow redirections, and allows
simultaneous downloads of multiple URLs.
* url() has a new method "libcurl" which handles more URL
schemes and follows redirections. The default method is
controlled by a new option url.method, which applies also to
the opening of URLs _via_ file() (which happens implicitly in
functions such as read.table.)
* When file() or url() is invoked with a https:// or ftps://
URL which the current method cannot handle, it switches to a
suitable method if one is available.
* (Windows.) The DLLs internet.dll and internet2.dll have been
merged. In this version it is safe to switch (repeatedly)
between the internal and Windows internet functions within an R
session.
The Windows internet functions are still selected by flag
- -internet2 or setInternet2(). This can be overridden for an
url() connection _via_ its new method argument.
download.file() has new method "wininet", selected as the default
by --internet2 or setInternet2().
* parent.env<- can no longer modify the parent of a locked
namespace or namespace imports environment. Contributed by Karl
Millar.
* New function isLoadedNamespace() for readability and speed.
* names(env) now returns all the object names of an environment
env, equivalently to ls(env, all.names = TRUE, sorted = FALSE)
and also to the names of the corresponding list,
names(as.list(env, all.names = TRUE)). Note that although
names() returns a character vector, the names have no particular
ordering.
* The memory manager now grows the heap more aggressively. This
reduces the number of garbage collections, in particular while
data or code are loaded, at the expense of slightly increasing
the memory footprint.
* New function trimws() for removing leading/trailing whitespace.
* cbind() and rbind() now consider S4 inheritance during S3
dispatch and also obey deparse.level.
* cbind() and rbind() will delegate recursively to methods::cbind2
(methods::rbind2) when at least one argument is an S4 object and
S3 dispatch fails (due to ambiguity).
* (Windows.) download.file(quiet = FALSE) now uses text rather
than Windows progress bars in non-interactive use.
* New function hsearch_db() in package utils for building and
retrieving the help search database used by help.search(), along
with functions for inspecting the concepts and keywords in the
help search database.
* New function .getNamespaceInfo(), a no-check version of
getNamespaceInfo() mostly for internal speedups.
* The help search system now takes \keyword entries in Rd files
which are not standard keywords (as given in KEYWORDS in the R
documentation directory) as concepts. For standard keyword
entries the corresponding descriptions are additionally taken as
concepts.
* New lengths() function for getting the lengths of all elements in
a list.
* New function toTitleCase() in package tools, tailored to package
titles.
* The matrix methods of cbind() and rbind() allow matrices as
inputs which have 2^31 or more elements. (For cbind(), wish of
PR#16198.)
* The default method of image() has an explicit check for a numeric
or logical matrix (which was always required).
* URLencode() will not by default encode further URLs which appear
to be already encoded.
* BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima()
fitted models, as nobs(mod) now gives the number of "used"
observations for such models. This fixes PR#16198, quite
differently than proposed there.
* The print() methods for "htest", "pairwise.htest" and
"power.htest" objects now have a digits argument defaulting to (a
function of) getOption("digits"), and influencing all printed
numbers coherently. Unavoidably, this changes the display of
such test results in some cases.
* Code completion for namespaces now recognizes all loaded
namespaces, rather than only the ones that are also attached.
* The code completion mechanism can now be replaced by a
user-specified completer function, for (temporary) situations
where the usual code completion is inappropriate.
* unzip() will now warn if it is able to detect truncation when
unpacking a file of 4GB or more (related to PR#16243).
* methods() reports S4 in addition to S3 methods; output is
simplified when the class argument is used. .S3methods() and
methods::.S4methods() report S3 and S4 methods separately.
* Higher order functions such as the apply functions and Reduce()
now force arguments to the functions they apply in order to
eliminate undesirable interactions between lazy evaluation and
variable capture in closures. This resolves PR#16093.
INSTALLATION and INCLUDED SOFTWARE:
* The \donttest sections of R's help files can be tested by
make check TEST_DONTTEST=TRUE .
* It is possible to request the use of system valgrind headers
_via_ configure option --with-system-valgrind-headers: note the
possible future incompatibility of such headers discussed in the
'R Installation and Administration' manual. (Wish of PR#16068.)
* The included version of liblzma has been updated to xz-utils
5.0.7 (minor bug fixes from 5.0.5).
* configure options --with-system-zlib, --with-system-bzlib and
- -with-system-pcre are now the default. For the time being there
is fallback to the versions included in the R sources if no
system versions are found or (unlikely) if they are too old.
Linux users should check that the -devel or -dev versions of
packages zlib, bzip2/libbz2 and pcre as well as
xz-devel/liblzma-dev (or similar names) are installed.
* configure by default looks for the texi2any script from texinfo
5.1 or later, rather than the makeinfo program. (makeinfo is a
link to the Perl script texi2any in texinfo 5.x.)
* R CMD INSTALL gains an option --built-timestamp=STAMP allowing
100% reproducible package building, thanks to Dirk Eddelbuettel.
UTILITIES:
* There is support for testing the \dontrun and \donttest parts of
examples in packages.
tools::testInstalledPackage() accepts new arguments
commentDontrun = FALSE and commentDonttest = FALSE.
R CMD check gains options --run-dontrun and --run-donttest.
* The HTML generated by tools::Rd2HTML() and tools::toHTML()
methods is now 'XHTML 1.0 Strict'.
* The compiler package's utility function setCompilerOptions() now
returns the old values invisibly. The initial optimization level
can also be set with the environment variable
R_COMPILER_OPTIMIZE.
* R CMD build adds a NeedsCompilation field if one is not already
present in the DESCRIPTION file.
* R CMD check gains option --test-dir to specify an alternative set
of tests to run.
* R CMD check will now by default continue with testing after many
types of errors, and will output a summary count of errors at the
end if any have occurred.
* R CMD check now checks that the Title and Description fields are
correctly terminated.
* R CMD check --as-cran now:
* checks a README.md file can be processed: this needs pandoc
installed.
* checks the existence and accessibility of URLs in the
DESCRIPTION, CITATION, NEWS.Rd and README.md files and in the
help files (provided the build has libcurl support).
* reports non-ASCII characters in R source files when there is
no package encoding declared in the DESCRIPTION file.
* reports (apparent) S3 methods exported but not registered.
* reports overwriting registered S3 methods from
base/recommended packages. (Such methods are replaced in the
affected package for the rest of the session, even if the
replacing namespace is unloaded.)
* reports if the Title field does not appear to be in title
case (see 'Writing R Extensions': there may be false
positives, but note that technical words should be
single-quoted and will then be accepted).
Most of these checks can also be selected by environment
variables: see the 'R Internals' manual.
C-LEVEL FACILITIES:
* New C API utility logspace_sum(logx[], n).
* Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by
default) to Rf_rbinom_mu etc. This requires packages using them
to be re-installed.
* .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so
arguments are duplicated if DUP = TRUE would do so. As their
help has long said, .Call() is much preferred.
* New entry point R_allocLD, like R_alloc but guaranteed to have
sufficient alignment for long double pointers.
* isPairList() now returns TRUE for DOTSXP.
WINDOWS BUILD CHANGES:
A number of changes to the Windows build system are in development.
The following are currently in place.
* Installation using external binary distributions of zlib, bzip2,
liblzma, pcre, libpng, jpeglib and libtiff is now required, and
the build instructions have been revised.
* A new make target rsync-extsoft has been added to obtain copies
of the external libraries from CRAN.
* Building the manuals now requires texi2any from texinfo 5.1 or
later. CRAN binary builds include the manuals, but by default
builds from source will not, and they will be accessed from CRAN.
See the comments in src/gnuwin32/MkRules.dist for how to specify
the location of texi2any.
* (Windows) Changes have been made to support an experimental
Windows toolchain based on GCC 4.9.2. The default toolchain
continues to be based on GCC 4.6.3, as the new toolchain is not
yet stable enough. A change to a new toolchain is expected
during the R 3.2.x lifetime.
PACKAGE INSTALLATION:
* (Windows) The use of macro ZLIB_LIBS in file src/Makevars.win
(which has not been documented for a long time) now requires an
external libz.a to be available (it is part of the 'goodies' used
to compile Windows binary packages). It would be simpler to use
- lz instead.
* The default for option pkgType on platforms using binary packages
is now "both", so source packages will be tried if binary
versions are not available or not up to date.
There are options for what install.packages(type = "both")
(possibly called _via_ update.packages()) will do if compilation
of a source package is desirable: see ?options (under utils).
If you intend not to accept updates as source packages, you
should use update.packages(type = "binary").
DEPRECATED AND DEFUNCT:
* download.file(method = "lynx") is defunct.
* Building R using the included versions of zlib, bzip2, xz and
PCRE is deprecated: these are frozen (bar essential bug-fixes)
and will be removed for R 3.3.0.
* The configure option --with-valgrind-instrumentation=3 has been
withdrawn, as it did not work with recent valgrind headers: it is
now treated as level 2.
* The MethodsList class in package methods had been deprecated in R
2.11.0 and is defunct now. Functions using it are defunct if
they had been deprecated in R 2.11.0, and are deprecated now,
otherwise.
BUG FIXES:
* Fixed two obscure bugs in pairlist subassignment, reported by
Radford Neal as part of pqR issue 16.
* Fixes for bugs in handling empty arguments and argument matching
by name in log().
* all.equal() gains methods for environments and refClasses.
* [<- and [[<- gain S4 data.frame methods to avoid corruption of S4
class information by the S3 methods.
* callNextMethod() should now work within a .local call when ... is
absent from formals(.local).
* dput(pairlist(x)) generates a call to the pairlist constructor
instead of the list constructor.
* Fix missing() when arguments are propagated through ... .
(PR#15707)
* eigen(m) now defaults to symmetric = TRUE even when the dimnames
are asymmetric if the matrix is otherwise symmetric. (PR#16151)
* Fix issues with forwarding ... through callGeneric() and
callNextMethod(). (PR#16141)
* callGeneric() now works after a callNextMethod().
* Subclass information is kept consistent when replacing an
ordinary S4 class with an "old class" _via_ the S4Class argument
to setOldClass(). Thus, for example, a data.frame is valid for a
list argument in the signature, and a factor is valid for vector
arguments.
* In qbeta() the inversion of pbeta() is much more sophisticated.
This works better in corner cases some of which failed completely
previously (PR#15755), or were using too many iterations.
* Auto-printing no longer duplicates objects when printing is
dispatched to a method.
* kmeans(x, k) would fail when nrow(x) >= 42949673. (Comment 6 of
PR#15364)
* 'Abbreviated' locale-specific day and month names could have been
truncated in those rare locales where there are the same as the
full names.
* An irrelevant warning message from updating subclass information
was silenced (the namespace would not be writable in this case).
* Mon Mar 09 2015 detlef.steuer@gmx.de
- Upstream release 3.1.3
- Most important
CHANGES IN R 3.1.3:
NEW FEATURES:
* The internal method of download.file() can now handle files
larger than 2GB on 32-bit builds which support such files (tested
on 32-bit R running on 64-bit Windows).
* kruskal.test() warns on more types of suspicious input.
* The as.dendrogram() method for "hclust" objects gains a check
argument protecting against memory explosion for invalid inputs.
* capabilities() has a new item long.double which indicates if the
build uses a long double type which is longer than double.
* nlm() no longer modifies the callback argument in place (a new
vector is allocated for each invocation, which mimics the
implicit duplication that occurred in R < 3.1.0); note that this
is a change from the previously documented behavior. (PR#15958)
* icuSetCollate() now accepts locale = "ASCII" which uses the basic
C function strcmp and so collates strings byte-by-byte in
numerical order.
* sessionInfo() tries to report the OS version in use (not just
that compiled under, and including details of Linux
distributions).
* model.frame() (used by lm() and many other modelling functions)
now warns when it drops contrasts from factors. (Wish of
PR#16119)
* install.packages() and friends now accept the value type =
"binary" as a synonym for the native binary type on the platform
(if it has one).
* Single source or binary files can be supplied for
install.packages(type = "both") and the appropriate type and
repos = NULL will be inferred.
* New function pcre_config() to report on some of the configuration
options of the version of PCRE in use. In particular, this
reports if regular expressions using \p{xx} are supported.
* (Windows.) download.file(cacheOK = FALSE) is now supported when
internet2.dll is used.
* browseURL() has been updated to work with Firefox 36.0 which has
dropped support for the -remote interface.
INSTALLATION and INCLUDED SOFTWARE:
* The included version of PCRE has been updated to 8.36.
* configure accepts MAKEINFO=texi2any as another way to ensure
texinfo 5.x is used when both 5.x and 4.x are installed.
UTILITIES:
* R CMD check now checks the packages used in \donttest sections of
the examples are specified in the DESCRIPTION file. (These are
needed to run the examples interactively.)
* R CMD check checks for the undeclared use of GNU extensions in
Makefiles, and for Makefiles with a missing final linefeed.
R CMD build will correct line endings in all Makefiles, not just
those in the src directory.
* R CMD check notes uses of library() and require() in package
code: see the section 'Suggested packages' of 'Writing R
Extensions' for good practice.
DEPRECATED AND DEFUNCT:
* The configure option --with-valgrind-instrumentation=3 is
deprecated and will be removed in R 3.2.0.
BUG FIXES:
* (Windows.) Rscript.exe was missing a manifest specifying the
modern style for common controls (e.g., the download progress
bar).
* If a package had extra documentation files but no vignette, the
HTML help system produced an empty index page.
* The parser now gives an error if a null character is included in
a string using Unicode escapes. (PR#16046)
* qr.Q() failed on complex arguments due to pre-3.0(!) typo.
(PR#16054)
* abs() failed with named arguments when the argument was complex.
(PR#16047)
* "noquote" objects may now be used as columns in dataframes.
(PR#15997)
* Some values with extremely long names were printed incorrectly.
(PR#15999)
* Extremely large exponents on zero expressed in scientific
notation (e.g. 0.0e50000) could give NaN. (PR#15976)
* download.file() reported downloaded sizes as 0KB if less than
1MB, only for R 3.1.2 and only on big-endian platforms.
* prompt() did not escape percent signs in the automatically
generated usage section of help files.
* drop.terms() dropped some of the attributes of the object it was
working with. (PR#16029)
* (Windows.) The command completion in Rgui.exe messed up the
console. (PR#15791)
* (Windows.) The choose.files() command returned a blank string
when the user asked for a single file but cancelled the request.
(PR#16074)
* Math2 S4 group generics failed to correctly dispatch "structure"-
and "nonStructure"-derived classes.
* loadNamespace() imposed undocumented restrictions on the
versionCheck parameter. (Reported by Geoff Lee.)
* Rare over-runs detected by AddressSanitizer in substr() and its
replacement version have been avoided.
_Inter alia_ that fix gives the documented behaviour for
substr(x, 1, 2) <- "" (subsequently reported as PR#16214).
* Loading packages incorrectly defining an S4 generic followed by a
function of the same name caused an erroneous cyclic namespace
dependency error.
* Declared vignette encodings are now always passed to the vignette
engine.
* Port Tomas Kalibera's fix from R-devel that restores the
loadMethod() fast path, effectively doubling the speed of S4
dispatch.
* power.t.test() and power.prop.test() now make use of the
extendInt option of uniroot() and hence work in more extreme
cases. (PR#15792)
* If a package was updated and attached when its namespace was
already loaded, it could end up with parts from one version and
parts from the other. (PR#16120)
* tools:::.Rdconv() didn't accept --encoding= due to a typo.
(PR#16121)
* Unix-alike builds without a suitable makeinfo were documented to
link the missing HTML manuals to CRAN, but did not.
* save(*, ascii=TRUE) and load() now correctly deal with NaN's.
(PR#16137)
* split.Date() retains fractional representations while avoiding
incomplete class propagation.
* R_ext/Lapack.h had not been updated for changes made by LAPACK to
the argument lists of its (largely internal) functions dlaed2 and
dlaed3. (PR#16157)
* RShowDoc("NEWS", "txt") had not been updated for the layout
changes of R 3.1.0.
* The xtfrm() method for class "Surv" has been corrected and its
description expanded.
* mode(x) <- y would incorrectly evaluate x before changing its
mode. (PR#16215)
* besselJ(1, 2^64) and besselY(..) now signal a warning, returning
NaN instead of typically segfaulting. (Issue 3 of PR#15554)
* HTML conversion of \href markup in .Rd files did not remove the
backslash from \% and so gave an invalid URL. In a related
change, the \ escape is now required in such URLs.
* Fri Dec 12 2014 sbahling@suse.com
- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
older SLE releases).
* Fri Oct 31 2014 detlef.steuer@gmx.de
- Upstream release 3.1.2
- Most important
CHANGES IN R 3.1.2:
NEW FEATURES:
* embedFonts() now defaults to format = "ps2write" for .ps and .eps
files. This is available in Ghostscript 9.x (since 2010) whereas
the previous default, format = "pswrite", was removed in
Ghostscript 9.10.
* For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
point mass at exp(mulog) rather than return NaN (for an error).
* capabilities() now reports if ICU is compiled in for use for
collation (it is only actually used if a suitable locale is set
for collation, and never for a C locale).
* (OS X only.) Package tcltk checks when loaded if it is linked
against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
component and the X11 libraries are installed. This allows more
informative error messages to be given advising the installation
of the missing component or of XQuartz.
The X11() device and X11-based versions of the data editor and
viewer (invoked by edit() and View() for data frames and matrices
from command-line R) check that the X11 libraries are installed
and if not advises installing XQuartz.
* icuSetCollate() allows locale = "default", and locale = "none" to
use OS services rather than ICU for collation.
Environment variable R_ICU_LOCALE can be used to set the default
ICU locale, in case the one derived from the OS locale is
inappropriate (this is currently necessary on Windows).
* New function icuGetCollate() to report on the ICU collation
locale in use (if any).
* utils::URLencode() was updated to use unreserved and reserved
characters from RFC 3986, <URL:
http://tools.ietf.org/html/rfc3986>, instead of RFC 1738.
* unique(warnings()) and c(warnings()) are now supported.
* The Bioconductor 'version' used by setRepositories() now defaults
to 3.0. (It can be set at runtime _via_ environment variable
R_BIOC_VERSION.)
INSTALLATION and INCLUDED SOFTWARE:
* The configure script reports on the more important
capabilities/options which will not be compiled in.
More types of external BLAS are recognized by name in that
report.
* When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
flag is placed earlier in the link commands used during
installation and when packages are installed: this helps ensure
that the current build has priority if an R shared library has
already been installed by e.g. install-libR in a library
mentioned in LDFLAGS (and not in 'your system's library
directory' as documented). (Wish of PR#15790.)
* LaTeX package upquote is no longer required for R's use of
inconsolata.
* (Windows only) If both 32 and 64 bit versions of R are installed,
the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
(To run 32 bit R, overwrite these files with copies of
bin/i386/Rfe.exe.)
UTILITIES:
* Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
the VignetteBuilder packages available even if they are listed in
Suggests, since they are needed to recognise and process
non-Sweave vignettes.
* R CMD check now reports empty importFrom declarations in a
NAMESPACE file, as these are common errors (writing
importFrom(Pkg) where import(Pkg) was intended).
* R CMD check now by default checks code usage directly on the
package namespace without loading and attaching the package and
its suggests and enhances. For good practice with packages in
the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'. For
use of lazy-data objects in the package's own code, see ?data.
BUG FIXES:
* dmultinom() did not handle non-finite probabilities correctly.
* prettyNum(x, zero.print=*) now also works when x contains NAs.
* A longstanding bug exhibited by nlminb() on Windows was traced to
a compiler bug in gcc 4.6.3; a workaround has been put in place.
(PR#15244 and PR#15914).
* Rendering of \command in HTML versions of help pages has been
improved: this is particularly evident on the help page for
INSTALL.
* as.hexmode(x) and as.octmode(x) now behave correctly for some
numeric x, e.g., c(NA, 1) or c(1, pi).
* drop1() failed if the scope argument had no variables to drop.
(PR#15935)
* edit() (and hence fix()) failed if an object had a non-character
attribute named "source" (an attribute that had been used in R
prior to version 2.14.0).
* callGeneric() could fail if the generic had ... as a formal
argument. (PR#15937).
* Forking in package parallel called C entry point exit in the
child. This was unsafe (_exit should have been called), and
could flush stdin of the main R process (seen most often on
Solaris).
As good practice, stdout is now flushed before forking a child.
* R objects such as list(`a\b` = 1) now print correctly.
* getAnywhere("C_pbinom") now returns correctly a single object
(rather than unlisting it).
* The confint() method for nls() fits failed it these has specified
parameter limits despite using an algorithm other than "port".
(PR#15960)
* Subclassing an S4 class failed if the class required arguments to
the generator, through its initialize() method.
* removeSource() did not properly handle expressions containing
arguments that were supplied as missing, e.g. x[i,]. (PR#15957)
* as.environment(list()) now works, and as.list() of such an
environment is now the same as list().
* Several tcltk functions failed when run in unusual environments.
(PR#15970)
* options(list()) now works (trivially). (PR#15979)
* merge(<dendrogram>, ..) now works correctly for two `independent'
dendrograms (PR#15648), and still compatibly via adjust = "auto"
e.g. for two branches of an existing dendrogram.
* The plot method for "hclust" objects gets an optional argument
check; When that is true (the default) it checks more carefully
for valid input.
* (Windows only) If a user chose to install 64 bit R but not 32 bit
R, the bin/R and bin/Rscript executables failed to run.
(PR#15981)
* Various possible buffer overruns have been prevented, and missed
memory protection added. (PR#15990)
* Rscript no longer passes --args to R when there are no extra
("user") arguments.
* objects like getClass("refClass")@prototype now print() and str()
without error.
* identical() now also looks at the S4 bit.
* hist(x, breaks) is more robust in adding a small fuzz to few
breaks when some are very large. (PR#15988)
* sub() and gsub() did not handle regular expressions like "\s{2,}"
properly if the text contained NA or non-ascii elements in a
UTF-8 locale. Part of this was due to a bug in the TRE library.
(PR#16009)
* RShowDoc("NEWS") now displays the PDF version.
* Matrices and arrays with last dimension zero did not print at all
or incompletely. (PR#16012)
* plot.histogram() and hence hist() now respect the xaxs, yaxs and
lab graphics parameters. (PR#16021)
* bw.SJ(x) and other bw.*() no longer segfault when x contains
non-finite values. (PR#16024)
* R CMD Rd2pdf unintentionally ignored its --os option.
* The internal method of download.file() was not reporting file
sizes and progress correctly on files larger than 2GB (inherited
from libxml2). This is corrected for 64-bit builds (32-bit
platforms may not support such files, but where possible will be
supported in future versions of R).
* Work around a bug in OS X Yosemite where key environment
variables may be duplicated causing issues in subprocesses. The
duplicates are now removed on R startup (via Rprofile).
(PR#16042)
* Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
latest XQuartz.
* Thu Jul 10 2014 detlef.steuer@gmx.de
- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
CHANGES IN R 3.1.1:
CHANGES IN R 3.1.1:
NEW FEATURES:
* When attach() reports conflicts, it does so compatibly with
library() by using message().
* R CMD Sweave no longer cleans any files by default, compatibly
with versions of R prior to 3.1.0. There are new options
- -clean, --clean=default and --clean=keepOuts.
* tools::buildVignette() and tools::buildVignettes() with clean =
FALSE no longer remove any created files. buildvignette() gains
a keep argument for more cleaning customization.
* The Bioconductor 'version' used by setRepositories() can now be
set by environment variable R_BIOC_VERSION at runtime, not just
when R is installed. (It has been stated that Bioconductor will
switch from 'version' 2.14 to 'version' 3.0 during the lifetime
of the R 3.1 series.)
* Error messages from bugs in embedded Sexpr code in Sweave
documents now report the source location.
* type.convert(), read.table() and similar read.*() functions get a
new numerals argument, specifying how numeric input is converted
when its conversion to double precision loses accuracy. The
default value, "allow.loss" allows accuracy loss, as in R
versions before 3.1.0.
* For some compilers, integer addition could overflow without a
warning. R's internal code for both integer addition and
subtraction is more robust now. (PR#15774)
* The function determining the default number of knots for
smooth.spline() is now exported, as .nknots.smspl().
* dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
for a = 0, b = 0, or infinite a and b (where they typically
returned NaN before).
* Many package authors report that the RStudio graphics device does
not work correctly with their package's use of dev.new(). The
new option dev.new(noRStudioGD = TRUE) replaces the RStudio
override by the default device as selected by R itself, still
respecting environment variables R_INTERACTIVE_DEVICE and
R_DEFAULT_DEVICE.
* readRDS() now returns visibly.
* Modifying internal logical scalar constants now results in an
error instead of a warning.
* install.packages(repos = NULL) now accepts http:// or ftp:// URLs
of package archives as well as file paths, and will download as
required. In most cases repos = NULL can be deduced from the
extension of the URL.
* The warning when using partial matching with the $ operator on
data frames is now only given when
options("warnPartialMatchDollar") is TRUE.
* Package help requests like package?foo now try the package foo
whether loaded or not.
* General help requests now default to trying all loaded packages,
not just those on the search path.
* Added a new function promptImport(), to generate a help page for
a function that was imported from another package (and presumably
re-exported, or help would not be needed).
INSTALLATION and INCLUDED SOFTWARE:
* configure option --with-internal-tzcode can now be used with
variable rsharedir.
* The included version of PCRE has been updated to 8.35.
* There is a new target make uninstall-libR to remove an installed
shared/static libR.
make install-libR now works if a sub-architecture is used,
although the user will need to specify libdir differently for
different sub-architectures.
* There is more extensive advice on which LaTeX packages are
required to install R or to make package manuals (as done by R
CMD check) in the 'Writing R Extensions' manual.
* Compilers/linkers were handling the visibility controls in
src/extra/xz inconsistently (and apparently in some cases
incorrectly), so it has been simplified. (PR#15327)
* (Windows) There is updated support for the use of ICU for
collation: see the 'R Installation and Administration Manual'.
BUG FIXES:
* dbinom(x, n), pbinom(), dpois(), etc, are slightly less
restrictive in checking if n is integer-valued. (Wish of
PR#15734.)
* pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
underflows for small x and ncp < 80, e.g, for pchisq(1e-5, df =
100, ncp = 1, log = TRUE). (Based on PR#15635 and a suggestion
by Roby Joehanes.)
* The s ("step into") command in the debugger would cause R to step
into expressions evaluated there, not just into functions being
debugged. (PR#15770)
* The C code used by strptime() rejected time-zone offsets of more
than +1200 (+1245, +1300 and +1400 can occur). (PR#15768)
* (Windows only.) png(type = "cairo", antialias = "gray") was not
accepted. (PR#15760)
* Use of save(..., envir=) with named objects could fail.
(PR#15758)
* Sweave() mis-parsed Sexpr expressions that contained backslashes.
(PR#15779)
* The return value from options(foo = NULL) was not the previous
value of the option. (PR#15781)
* enc2utf8() and enc2native() did not always mark the encoding of
the return values when it was known.
* dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows
to -Inf for large mu, thanks to a suggestion from Alessandro
Mammana (MPI MolGen, Berlin).
* pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
a small x-region) because of denormalized numbers. Also,
pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
time".
* The "CRAN" filter (see available.packages()) no longer removes
duplicates other than of packages on CRAN, and does not fail if
there is no CRAN repository in getOption("repos").
* The device listing from dev2bitmap() and bitmap() was truncated
to 1000 characters: modern versions of GhostScript on most
platforms have many more devices.
* (Windows.) Commands such as Sys.which() and pipe() which needed
to find the full path to a command could segfault if the 'long'
path name was much longer than the 'short' path name (which
Sys.which() returns), as the behaviour of the Windows API call
had changed.
* R CMD build will fail with an error if one of the packages
specified in the VignetteBuilder field is not installed.
(Without loading those packages it cannot be ascertained which
files are intended to be vignettes. This means that the
VignetteBuilder packages have to be installed for package
checking too.) (Wish of PR#15775.)
* Misguided attempts to use chull() with non-finite points now give
an error (related to PR#15777).
* For a formula with exactly 32 variables the 32nd variable was
aliased to the intercept in some C-level computations of terms,
so that for example attempting to remove it would remove the
intercept instead (and leave a corrupt internal structure).
(PR#15735)
* anyDuplicated() silently returned wrong values when the first
duplicate was at an index which was too large to be stored in an
integer vector (although a lot of RAM and patience would have
been needed to encounter this).
* tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
one line.
* Hexadecimal constants such as 0x110p-5L which were incorrectly
qualified by L were parsed incorrectly since R 3.0.0, with a
slightly garbled warning. (PR#15753)
* system() returned success on some platforms even if the system
was unable to launch a process. (PR#15796)
* (Windows Rgui console.) Unbuffered output was sometimes not
output immediately if the prompt was not on the last line of the
console.
* The built-in help server did not declare the encoding for the
DESCRIPTION or other text files to be the package encoding, so
non-ASCII characters could be displayed incorrectly.
* R is now trying harder to not cleanup child processes that were
not spawned by mcparallel() on platforms that provide information
about the source process of the SIGCHLD signal. This allows 3rd
party libraries to manage the exit status of children that they
spawn without R interfering.
* mcmapply() was only parallelizing if the number of jobs was
bigger than the number of cores. It now parallelizes if the
number of jobs is more than one.
* Auto-printing would re-evaluate its argument when trying to
dispatch to a print method. This is now avoided when possible.
* Unserializing (including load() and readRDS()) could silently
return incorrect numeric values from ASCII saves if there was a
read error.
* getParseData() could return incorrect values for the parents of
some elements. (Reported by Andrew Redd.)
* Attempting to use data frames of 2^31 or more rows with merge()
or to create a merged data frame of that size now gives a clearer
error message.
* parse() did not check its file argument was a connection if it
was not a character string, so e.g. parse(FALSE) attempted to
read from stdin.
Nor did dump() and dput().
* The "help.try.all.packages" option was ignored when the shortcut
syntax for help was used, e.g. ?foo.
* A potential segfault in string allocation has been fixed. (Found
by Radford Neal.)
* Potential memory protection errors in sort() and D() have been
fixed. (Found by Radford Neal.)
* Fixed a lack of error checking in graphics event functions.
(Found by Radford Neal; a different patch used here than the one
in pqR.)
* numericDeriv() sometimes miscalculated the gradient. (PR#15849,
reported originally by Radford Neal)
* Fri Jun 20 2014 darin@darins.net
- added parallel provides
* Fri May 09 2014 detlef.steuer@gmx.de
- Removed / commented out symlink to %{_bindir}/r
new package 'littler' should be used instead for packages
that need /usr/bin/r