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| Name: R-boot | Distribution: SUSE Linux Enterprise 15 SP5 |
| Version: 1.3.28 | Vendor: openSUSE |
| Release: bp155.5.57 | Build date: Mon May 22 12:37:55 2023 |
| Group: Unspecified | Build host: armbuild22 |
| Size: 690698 | Source RPM: R-base-4.2.2-bp155.5.57.src.rpm |
| Packager: https://bugs.opensuse.org | |
| Url: http://www.r-project.org/ | |
| Summary: Package provides recommended R-boot | |
This packages provides R-boot, one of the recommended packages.
GPL-2.0-only OR GPL-3.0-only
* Mon Oct 31 2022 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.2.2:
NEW FEATURES:
* tools::Rdiff(useDiff = TRUE) checks for the presence of an
external diff command and switches to useDiff = FALSE if none is
found. This allows R CMD Rdiff to always work.
* On Windows, environment variable R_LIBCURL_SSL_REVOKE_BEST_EFFORT
can be used to switch to only 'best-effort' SSL certificate
revocation checks with the default "libcurl" download method.
This reduces security, but may be needed for downloads to work
with MITM proxies (PR#18379).
* (macOS) The run-time check for libraries from XQuartz for X11 and
Tcl/Tk no longer uses otool from the Apple Developer Tools
(PR#18400).
* The LaTeX style for producing the PDF manuals, Rd.sty, now loads
the standard amsmath, amsfonts and amssymb packages for greater
coverage of math commands in the Rd \eqn and \deqn macros. The
\mathscr LaTeX command is also provided (via the mathrsfs
package, if available, or the amsfonts bundle otherwise),
fulfilling the wish of PR#18398.
* (Windows) The default format of readClipboard() and
writeClipboard() has been changed to 13 (CF_UNICODETEXT).
INSTALLATION on a UNIX-ALIKE:
* The PDF manuals (if built) can be compacted by the new target
make compact-pdf (at the top level or in directory doc/manual).
* There is now configure support for LLVM clang 15 on Linux, which
defaults to position-independent (PIE) executables whereas
gfortran does not.
* Many small changes to ease compilation (and suppress warnings)
with LLVM clang 15.
BUG FIXES:
* Rscript -e would fail if stdin were closed (Reported by Henrik
Bengtsson.)
* qt(*, log.p=TRUE) in outer tails no longer produces NaN in its
final steps, thus fixing PR#18360.
* tools::Rd2latex() now escapes hashes and ampersands when writing
URLs, fixing LaTeX errors with such URLs in \tabular.
* When isGeneric(f, fdef=*) is used with mismatching names, the
warning is better understandable; reported (with fix) in PR#18370
by Gabe Becker.
* poly(x, n) now works again (and is now documented) when x is a
"Date" or "POSIXct" object, or of another class while fulfilling
mode(x) == "numeric". This also enables poly(x, *, raw=TRUE) for
such variables. Reported by Michael Chirico to R-devel.
* write.table(), write.csv() and write.csv2() restore their
numerical precision (internal equivalent of digits = 15) after an
interrupt (PR#18384).
* One can now read also byte FF from a clipboard connection
(PR#18385).
* source("") and source(character()) now give more helpful error
messages.
* R CMD check --as-cran set _R_CHECK_TIMINGS_ too late to have the
intended effect.
* as.POSIXlt(x) now also works with very large dates x, fixing
PR#18401 reported by Hannes M"uhleisen.
* Files can now be extracted even from very large zip archives
(PR#18390, thanks to Martin Jakt).
* Non-finite objects of class "POSIXlt" are now correctly coerced
to classes "Date" and "POSIXct"; following up on the extension to
format() them correctly.
* Added methods for is.finite(), is.infinite() and is.nan() for
"POSIXlt" date-time objects.
* Thu Jun 23 2022 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.2.1:
NEW FEATURES:
* New function utils::findCRANmirror() to find out if a CRAN mirror
has been selected, otherwise fallback to the main site. This
behaves in the same way as tools::CRAN_package_db() and is
intended for packages wishing to access CRAN for purposes other
than installing packages.
The need for this was shown by a day when the main CRAN website
was offline and a dozen or so packages which had its URL
hardcoded failed their checks.
INSTALLATION on a UNIX-ALIKE:
* The libraries searched for by --with-blas (without a value) now
include BLIS (after OpenBLAS but before ATLAS). And on macOS,
the Accelerate framework (after ATLAS). (This is patterned after
the AX_BLAS macro from the Autoconf Archive.)
* The included LAPACK sources have been updated to 3.10.1.
UTILITIES:
* The (full path to) the command tidy to be used for HTML
validation can be set by environment variable R_TIDYCMD.
* Setting environment variable _R_CHECK_RD_VALIDATE_RD2HTML_ to a
false value will override R CMD check --as-cran and turn off HTML
validation. This provides a way to circumvent a problematic
tidy.
The 2006 version that ships with macOS is always skipped.
C-LEVEL FACILITIES:
* The undocumented legacy declarations of Sint, Sfloat, SINT_MAX
and SINT_MIN in header R.h are deprecated.
BUG FIXES:
* fisher.test(d) no longer segfaults for "large" d; fixing PR#18336
by preventing/detecting an integer overflow reliably.
* tar(., files=*) now produces correctly the warning about invalid
uid or gid of files, fixing PR#18344, reported by Martin Morgan.
* tk_choose.files() with multi = FALSE misbehaved on paths
containing spaces (PR#18334) (regression introduced in R 4.0.0).
* sort(x, partial = ind, *) now works correctly notably for the
non-default na.last = FALSE or TRUE, fixing PR#18335 reported by
James Edwards.
* Environment variable _R_CHECK_XREFS_REPOSITORIES_ is only used
for checking .Rd cross-references in R CMD check (as documented)
and not for other uses looking for a CRAN mirror.
* The search for a CRAN mirror when checking packages now uses
getOption("repos") if that specifies a CRAN mirror, even when it
does not also specify all three Bioconductor repositories (as was
previously required).
* The HTML code generated by tools::Rd2HTML() has been improved to
pass tidy 5.8.0.
* Fri Apr 22 2022 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.2.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* The formula method of aggregate() now matches the generic in
naming its first argument x (resolving PR#18299 by Thomas
Soeiro).
This means that calling aggregate() with a formula as a named
first argument requires name formula in earlier versions of R and
name x now, so portable code should not name the argument (code
in many packages did).
* Calling && or || with either argument of length greater than one
now gives a warning (which it is intended will become an error).
* Calling if() or while() with a condition of length greater than
one gives an error rather than a warning. Consequently,
environment variable _R_CHECK_LENGTH_1_CONDITION_ no longer has
any effect.
* Windows users should consult the WINDOWS section below for some
profound changes including
* Support for 32-bit builds has been dropped.
* UTF-8 locales are used where available.
* The default locations for the R installation and personal
library folder have been changed.
Thanks to Tomas Kalibera for months of work on the Windows port
for this release.
NEW FEATURES:
* matrix(x, n, m) now warns in more cases where length(x) differs
from n * m, as suggested by Abby Spurdle and Wolfgang Huber in
Feb 2021 on the R-devel mailing list.
This warning can be turned into an error by setting environment
variable _R_CHECK_MATRIX_DATA_ to TRUE: R CMD check --as-cran
does so unless it is already set.
* Function file_test() in package utils gains tests for symlinks,
readability and writability.
* capabilities("libxml") is now false.
The description of capabilities("http/ftp") now reflects that it
refers to the default method, no longer the internal one.
* simplify2array() gains an except argument for controlling the
exceptions used by sapply().
* Environment variables R_LIBS_USER and R_LIBS_SITE are both now
set to the R system default if unset or empty, and can be set to
NULL to indicate an empty list of user or site library
directories.
* The warning for axis()(-like) calls in cases of relatively small
ranges (typically in log-scale situations) is slightly improved
_and_ suppressed from explicit calls to .axisPars() as has always
been the intention.
* The contrasts setter function `contrasts<-` gains an explicit
default how.many = NULL rather than just using missing(how.many).
* grid.pretty() gains a new optional argument n = 5.
* There is a new function .pretty() with option bounds as a
technical-utility version of pretty(). It and pretty() gain a
new argument f.min with a better than back-compatible default.
* Function grDevices::axisTicks() and related functions such as
graphics::axis() work better, notably for the log scale; partly
because of the pretty() improvements, but also because care is
taken e.g., when ylim is finite but diff(ylim) is infinite.
* nclass.FD() gains a digits option.
* The R Mathlib internal C function bd0() (called indirectly from a
dozen probability density and distribution functions such as
dpois(), dbinom(), dgamma(), pgamma() _etc_) has been
complemented by a more sophisticated and (mostly) more accurate C
function ebd0(), currently called only by internal dpois_raw()
improving accuracy for R level dpois() and potentially others
calling it such as dnbinom(), dgamma() or pgamma(). (Thanks to
Morten Welinder's PR#15628.)
* write.ftable() gains sep = " " argument as suggested by Thomas
Soeiro.
* The names of the locale categories supported by R's
Sys.getlocale() and Sys.setlocale() are now provided by variable
.LC.categories in the base namespace.
* The Date and POSIXt methods for hist() and the histogram method
for plot() now also use the new default col = "lightgray" in
consistency with the corresponding change to hist()'s default for
R 4.0.0.
* hist.default() gains new fuzz argument, and the histogram plot
method no longer uses fractional axis ticks when displaying
counts ("Frequency").
* mapply() and hence Map() now also obey the "max-or-0-if-any"
recycling rule, such that, e.g., Map(`+`, 1:3, 1[0]) is valid
now.
* as.character(<obj>) for "hexmode" or "octmode" objects now
fulfils the important basic rule as.character(x)[j] ===
as.character(x[j]).
* The set utility functions, notably intersect() have been tweaked
to be more consistent and symmetric in their two set arguments,
also preserving a common mode.
* substr(ch, start,end) <- new now e.g., preserves names(ch); ditto
for substring(), thanks to a patch from Brodie Gaslam.
* plot(<lm>) gains a extend.ylim.f argument, in partial response to
PR#15285; further PR#17784 is fixed thanks to several
contributors and a patch by Elin Waring. The Cook's dist
contours get customizable via cook.col and cook.lty with a
different default color and their legend is nicer by default and
customizable via cook.legendChanges.
* Attempting to subset an object that is not subsettable now
signals an error of class notSubsettableError. The
non-subsettable object is contained in the object field of the
error condition.
* Subscript-out-of-bounds errors are now signaled as errors of
class subscriptOutOfBoundsError.
* Stack-overflow errors are now signaled as errors inheriting from
class stackOverflowError. See ?stackOverflowError for more
details.
* New partly experimental Sys.setLanguage() utility, solving the
main problem of PR#18055.
* gettext() and gettextf() get a new option trim = TRUE which when
set to false allows translations for strings such as "Execution
halted\n" typical for C code.
* An experimental implementation of hash tables is now available.
See ?hashtab for more details.
* identical() gains a extptr.as.ref argument for requesting that
external pointer objects be compared as reference objects.
* reorder() gets an argument decreasing which it passes to sort()
for level creation; based on the wish and patch by Thomas Soeiro
in PR#18243.
* as.vector() gains a data.frame method which returns a simple
named list, also clearing a long standing 'FIXME' to enable
as.vector(<data.frame>, mode="list"). This breaks code relying
on as.vector(<data.frame>) to return the unchanged data frame.
* legend() is now vectorized for arguments cex, x.intersp, and
text.width. The latter can now also be specified as a vector
(one element for each column of the legend) or as NA for
computing a proper column wise maximum value of strwidth(legend).
The argument y.intersp can be specified as a vector with one
entry for each row of the legend.
legend() also gains new arguments title.cex and title.font.
Thanks to Swetlana Herbrandt.
* Deparsing no longer remaps attribute names dim, dimnames, levels,
names and tsp to historical S-compatible names (which structure()
maps back).
* sample() and sample.int() have additional sanity checks on their
size and n arguments.
all.equal.numeric() gains a sanity check on its tolerance
argument - calling all.equal(a, b, c) for three numeric vectors
is a surprisingly common error.
mean(na.rm =), rank(na.last =), barplot(legend.text =),
boxplot(), contour(drawlabels =), polygon(border =) and
methods::is(class2 =) have more robust sanity checks on their
arguments.
R CMD Rd2pdf (used by R CMD check) has a more robust sanity check
on the format of \alias{} commands.
* psigamma(x, deriv) for negative x now also works for deriv = 4
and 5; their underlying C level dpsifn() is documented in
'Writing R Extensions'.
* The HTML help system now uses HTML5 (wish of PR#18149).
* ks.test() now provides exact p-values also with ties and MC
p-values in the two-sample (Smirnov) case. By Torsten Hothorn.
* ks.test() gains a formula interface, with y ~ 1 for the
one-sample (Kolmogorov) test and y ~ group for the two-sample
(Smirnov) test. Contributed by Torsten Hothorn.
* The return value from ks.test() now has class c("ks.test",
"htest") - packages using try() need to take care to use
inherits() and not == on the class.
* New functions psmirnov(), qsmirnov() and rsmirnov() in package
stats implementing the asymptotic and exact distributions of the
two-sample Smirnov statistic.
* iconv() now allows sub = "c99" to use C99-style escapes for UTF-8
inputs which cannot be converted to encoding to.
* In a forward pipe |> expression it is now possible to use a named
argument with the placeholder _ in the rhs call to specify where
the lhs is to be inserted. The placeholder can only appear once
on the rhs.
* The included LAPACK sources have been updated to version 3.10.0,
except for the four Fortran 77 routines which 3.10.0 has
re-implemented in Fortran 90 (where the older versions have been
retained as the R build process does not support Fortran 90).
* path.expand() and most other uses of tilde expansion now warn if
a path would be too long if expanded. (An exception is
file.exists(), which silently returns false.)
* trunc(<Date>, *) now supports units = "months" or "years" for
consistency with the POSIXt method, thanks to Dirk Eddelbuettel's
proposal in PR#18099.
* list2DF() now checks that its arguments are of the same length,
rather than use recycling.
* The HTML help system has several new features: LaTeX-like math
can be typeset using either KaTeX or MathJax, usage and example
code is highlighted using Prism, and for dynamic help the output
of examples and demos can be shown within the browser if the
knitr package is installed. These features can be disabled by
setting the environment variable _R_HELP_ENABLE_ENHANCED_HTML_ to
a false value.
GRAPHICS:
* The graphics engine version, R_GE_version, has been bumped to 15
and so packages that provide graphics devices should be
reinstalled.
* The grid package now allows the user to specify a "vector" of
pattern fills. The fill argument to gpar() accepts a list of
gradients and/or patterns and the functions linearGradient(),
radialGradient(), and pattern() have a new group argument.
Points grobs (data symbols) can now also have a pattern fill.
The grobCoords() function now returns a more informative and
complex result.
* The grid package has new functions for drawing isolated groups:
grid.group(), grid.define(), and grid.use(). These functions add
compositing operators and affine transformations to R's graphics
capabilities.
The grid package also has new functions for stroking and filling
paths: grid.stroke(), grid.fill(), and grid.fillStroke().
A new function as.path() allows the user to specify the fill rule
for a path that is to be used for clipping, stroking, or filling;
available options are "winding" and "evenodd". A new function
as.mask() allows the user to specify the type of a mask;
available options are "alpha" and "luminance".
These new features are only supported so far (at most) on the
Cairo-based graphics devices and on the pdf() device.
* dev.capabilities() reports on device support for the new
features.
* par() now warns about unnamed non-character arguments to prevent
misuse such as {usr <- par("usr"); par(usr)}.
INSTALLATION:
* Facilities for accessing ftp:// sites are no longer tested
(except _pro tem_ for curlGetHeaders()) as modern browsers have
removed support.
* R can now be built with DEFS = -DSTRICT_R_HEADERS .
PACKAGE INSTALLATION:
* R CMD INSTALL no longer tangles vignettes. This completes an R
CMD build change in R 3.0.0 and affects packages built before R
3.0.2. Such packages should be re-made with R CMD build to have
the tangled R code of vignettes shipped with the tarball.
* USE_FC_LEN_T will become the default: this uses the correct
prototypes for Fortran BLAS/LAPACK routines called from C/C++,
and requires adjustment of most such calls - see 'Writing R
Extensions' SS6.6.2. (This has been supported since R 3.6.2.)
* Package installation speed for packages installed with
keep.source has been improved. This resolve the issue reported by
Ofek Shilon in PR#18236.
UTILITIES:
* R CMD check can optionally report files/directories left behind
in home, /tmp (even though TMPDIR is set) and other directories.
See the "R Internals" manual for details.
* R CMD check now reports byte-compilation errors during
installation. These are not usually fatal but may result in
parts of the package not being byte-compiled.
* _R_CHECK_DEPENDS_ONLY_ can be applied selectively to examples,
tests and/or vignettes in R CMD check: see the "R Internals"
manual.
* _R_CHECK_SRC_MINUS_W_IMPLICIT_ now defaults to true: recent
versions of Apple clang on macOS have made implicit function
declarations in C into a compilation error.
* R CMD check --as-cran makes use of the environment variable
AUTORECONF. See the "R Internals" manual SS8 for further details.
* R CMD check --use-valgrind also uses valgrind when re-building
vignettes as some non-Sweave vignettes unhelpfully comment out
all their code when R CMD check runs vignettes.
* Errors in re-building vignettes (unless there are LaTeX errors)
are reported by R CMD check as ERROR rather than WARNING when
running vignettes has been skipped (as it frequently is in CRAN
checks and by --as-cran).
* R CMD Rd2pdf gains a --quiet option that is used by R CMD build
when building the PDF package manual.
* R CMD Rd2pdf now always runs LaTeX in batch mode, consistent with
Texinfo >= 6.7. The --batch option is ignored.
* R CMD build and R CMD check now include the Rd file name and line
numbers in the error message of an \Sexpr evaluation failure.
* For packages using the \doi Rd macro (now an install-time \Sexpr)
but no other dynamic Rd content, R CMD build now produces a
smaller tarball and is considerably faster - skipping temporary
package installation.
C-LEVEL FACILITIES:
* The non-API header R_ext/R-ftp-http.h is no longer provided, as
the entry points it covered are now all defunct.
* A number of non-API declarations and macro definitions have been
moved from the installed header Rinternals.h to the internal
header Defn.h. Packages that only use entry points and
definitions documented to be part of the API as specified in
'Writing R Extensions' SS6 should not be affected.
* The macro USE_RINTERNALS no longer has any effect when compiling
package code. Packages which also use R_NO_REMAP will need to
ensure that the remapped names are used for calls to API
functions that were formerly also made available as macros.
* The deprecated legacy S-compatibility macros PROBLEM, MESSAGE,
ERROR, WARN, WARNING, RECOVER, ... are no longer defined in
R_exts/RS.h (included by R.h). Replace these by calls to
Rf_error and Rf_warning (defined in header R_ext/Error.h included
by R.h).
Header R_ext/RS.h no longer includes R_ext/Error.h.
* Header R_ext/Constants.h (included by R.h) when included from C++
now includes the C++ header cfloat rather than the C header
float.h (now possible as C++11 is required).
* The legacy S-compatibility macros DOUBLE_* in R_ext/Constants.h
(included by R.h) are deprecated.
* The deprecated S-compatibility macros SINGLE_* in
R_ext/Constants.h (included by R.h) have been removed.
* R_Calloc, R_Free and R_Realloc are preferred to their unprefixed
forms and error messages now use the prefix. These forms were
introduced in R 3.4.0 and are available even when
STRICT_R_HEADERS is defined.
* rmultinom has been documented in 'Writing R Extensions' SS6 so is
now part of the R API.
* Similarly, Rtanpi, called from R level tanpi() is now part of the
R API.
* The long-deprecated, undocumented and non-API entry point call_R
is no longer declared in R_ext/RS.h (included by R.h).
* The header S.h which has been unsupported since Jan 2016 has been
removed. Use R.h instead.
DEPRECATED AND DEFUNCT:
* The (non-default and deprecated) method = "internal" for
download.file() and url() no longer supports http:// nor ftp://
URIs. (It is used only for file:// URIs.)
On Windows, download.file(method = "wininet") no longer supports
ftp:// URIs. (It is no longer the default method, which is
"libcurl" and does.)
On Windows, the deprecated method = "wininet" now gives a warning
for http:// and https:// URIs for both download.file() and url().
(It is no longer the default method.)
* On Windows, the command-line option --max-mem-size and
environment variable R_MAX_MEM_SIZE are defunct. The memory
allocation limit was important for 32-bit builds, but these are
no longer supported.
* default.stringsAsFactors() is now formally deprecated, where that
was only mentioned on its regular help page, previously. So it
now gives a warning if called.
* unix.time() is defunct now; it had been deprecated since R 3.4.0.
BUG FIXES:
* Setting digits = 0 in format(), print.default() (and hence
typically print()) or options() is again invalid. Its behaviour
was platform-dependent, and it is unclear what "zero significant
digits" should mean (PR#18098).
* Messages from C code in the cairo section of package grDevices
are now also offered for translation, thanks to Michael Chirico's
PR#18123.
* mean(x) with finite x now is finite also without "long.double"
capability.
* R CMD Rd2pdf no longer leaves an empty build directory behind
when it aborts due to an already existing output file. (Thanks
to Sebastian Meyer's PR#18141.)
* density(x, weights = w, na.rm = TRUE) when anyNA(x) is true, now
removes weights "in parallel" to x, fixing PR#18151, reported by
Matthias Gondan. Additionally, it gets a subdensity option.
* Conversion of \Sexpr[]{<expR>} to LaTeX or HTML no longer
produces long blocks of empty lines when <expR> itself contains
several lines all producing empty output. Thanks to a report and
patch by Ivan Krylov posted to R-devel.
* R CMD build no longer fails if a package vignette uses child
documents and inst/doc exists. (Thanks to Sebastian Meyer's
PR#18156.)
* When an R documentation ('help' source) file man/foo.Rd in a
package has \donttest{..} examples with a syntax error, it is now
signalled as ERROR and with correct line numbers relating to the
* -Ex.R file, thanks to Duncan Murdoch and Sebastian Meyer's
reports and patch proposals in PR#17501.
* Improved determination of the correct translation domain in
non-base packages, addressing the combination of PR#18092 and
PR#17998 (#c6) with reports and _augmented_ patch #2904 by
Suharto Anggono.
Note that "R-base" is no longer the default domain e.g., for
top-level calls to gettext(); rather translation needs explicit
domain = * specification in such cases.
* identical(attrib.as.set=FALSE) now works correctly with data
frames with default row names (Thanks to Charlie Gao's PR#18179).
* txtProgressBar() now enforces a non-zero width for argument char,
without which no progress can be visible.
* dimnames(table(d)) is more consistent in the case where d is a
list with a single component, thanks to Thomas Soeiro's report to
R-devel.
Further, table(d1, d2) now gives an error when d1 and d2 are data
frames as suggested by Thomas in PR#18224.
* Fix for drawing semi-transparent lines and fills on the native
Windows graphics device (PR#18219 and PR#16694). Thanks to Nick
Ray for helpful diagnosis on Bugzilla.
* The deparser now wraps sub-expressions such as if(A) .. with
parentheses when needed; thanks to Duncan Murdoch's PR#18232 and
Lionel Henry's patches there.
* remove.packages() no longer tries to uninstall Priority: base
packages, thanks to a report and suggestions by Colin Fay in
PR#18227.
* win.metafile() now has xpinch and ypinch arguments so that the
user can override Windows' (potentially wrong) guess at device
dimensions.
* x[i] and x[[i]] for non-integer i should now behave in all cases
as always documented: the index used is equivalent to
as.integer(i) unless that would overflow where trunc(i) is used
instead; thanks to Suharto Anggono's report and patch proposals
in PR#17977.
* asOneSidedFormula() now associates the resulting formula with the
global environment rather than the evaluation environment created
for the call.
* <bibentry>$name now matches the field name case-insensitively,
consistent with bibentry() creation and the replacement method.
* cbind() failed to detect some length mismatches with a mixture of
time-series and non-time-series inputs.
* The default LaTeX style file Sweave.sty used by the RweaveLatex
driver no longer loads the obsolete ae package; thanks to a
report by Thomas Soeiro in PR#18271. Furthermore, it now skips
\usepackage[T1]{fontenc} for engines other than pdfTeX (if
detected) or if the new [nofontenc] option is used.
* smooth.spline() now stores its logical cv argument more safely,
fixing a rare bug when printing, and also stores n.
* smooth.spline(x,y,*) now computes the cv.crit statistic
correctly, also when is.unsorted(x), fixing PR#18294.
* The data.frame method of rbind() now warns when binding
not-wholly-recycling vectors, by analogy to the default method
(for matrices).
* setAs() finds the correct class for name to when multiple
packages define a class with that name. Thanks to Gabor Csardi
for the report.
* Fix for detaching a package when two classes of the same name are
present in method signatures for the same generic. Thanks to
Gabor Csardi for the report.
* match.arg("", c("", "a", "B")) gives a better error message, in
part from PR#17959, thanks to Elin Waring.
* R CMD Sweave --clean no longer removes pre-existing files or
subdirectories (PR#18242).
* The quartz() device no longer splits polylines into subpaths.
That has caused narrowly-spaced lines with many points to always
look solid even when dashed line type was used due to dash phase
restarts.
* Deparsing constructs such as quote(1 + `!`(2) + 3) works again as
before R 3.5.0, thanks to the report and patch in PR#18284 by
Suharto Anggono.
* as.list(f) for a factor f now keeps names(f), fixing PR#18309.
* qbeta(.001, .9, .009) and analogous qf() calls now return a
correct value instead of NaN or wrongly 1, all with a warning;
thanks to the report by Ludger Goeminne in PR#18302.
* plot.lm() failed to produce the plot of residuals vs. factor
levels (i.e., which=5 when leverages are constant) for models
with character predictors (PR#17840).
* interaction.plot(..., xtick = TRUE) misplaced the x-axis line
(PR#18305).
* Not strictly fixing a bug, format()ing and print()ing of
non-finite Date and POSIXt values NaN and +/-Inf no longer show
as NA but the respective string, e.g., Inf, for consistency with
numeric vector's behaviour, fulfilling the wish of PR#18308.
* R CMD check no longer runs test scripts generated from
corresponding .Rin files twice and now signals an ERROR if
processing an .Rin script fails.
* tools::Rd2txt() used for plain-text help pages now renders \hrefs
(if tools::Rd2txt_options(showURLs = TRUE)) and \urls with
percent-encoding and standards-compliant delimiting style (angle
brackets and no URL: prefix). \email is now rendered with a
mailto: prefix.
* Fri Mar 11 2022 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.1.3:
NEW FEATURES:
* The default version of Bioconductor has been changed to 3.14.
(This is used by setRepositories and the menus in GUIs.)
UTILITIES:
* R CMD check --as-cran has a workaround for a bug in versions of
file up to at least 5.41 which mis-identify DBF files last
changed in 2022 as executables.
C-LEVEL FACILITIES:
* The legacy S-compatibility macros SINGLE_* in R_ext/Constants.h
(included by R.h) are deprecated and will be removed in R 4.2.0.
BUG FIXES:
* Initialization of self-starting nls() models with initialization
functions following the pre-R-4.1.0 API (without the ...
argument) works again for now, with a deprecation warning.
* Fixed quoting of ~autodetect~ in Java setting defaults to avoid
inadvertent user lookup due to leading ~, reported in PR#18231 by
Harold Gutch.
* substr(., start, stop) <- v now treats _negative_ stop values
correctly. Reported with a patch in PR#18228 by Brodie Gaslam.
* Subscripting an array x without dimnames by a
length(dim(x))-column character matrix gave "random" non-sense,
now an error; reported in PR#18244 by Mikael Jagan.
* ...names() now matches names(list(...)) closely, fixing PR#18247.
* all.equal(*, scale = s) now works as intended when length(s) > 1,
partly thanks to Michael Chirico's PR#18272.
* print(x) for long vectors x now also works for named atomic
vectors or lists and prints the correct number when reaching the
getOption("max.print") limit; partly thanks to a report and
proposal by Hugh Parsonage to the R-devel list.
* all.equal(<selfStart>, *) no longer signals a deprecation
warning.
* reformulate(*, response=r) gives a helpful error message now when
length(r) > 1, thanks to Bill Dunlap's PR#18281.
* Modifying globalCallingHandlers inside withCallingHandlers() now
works or fails correctly, thanks to Henrik Bengtsson's PR#18257.
* hist(<Date>, breaks = "days") and hist(<POSIXt>, breaks = "secs")
no longer fail for inputs of length 1.
* qbeta(.001, .9, .009) and similar cases now converge correctly
thanks to Ben Bolker's report in PR#17746.
* window(x, start, end) no longer wrongly signals "'start' cannot
be after 'end'", fixing PR#17527 and PR#18291.
* data() now checks that its (rarely used) list argument is a
character vector - a couple of packages passed other types and
gave incorrect results.
* which() now checks its arr.ind argument is TRUE rather coercing
to logical and taking the first element - which gave incorrect
results in package code.
* model.weights() and model.offset() more carefully extract their
model components, thanks to Ben Bolker and Tim Taylor's R-devel
post.
* list.files(recursive = TRUE) now shows all broken symlinks
(previously, some of them may have been omitted, PR#18296).
* Mon Nov 01 2021 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.1.2:
C-LEVEL FACILITIES:
* The workaround in headers R.h and Rmath.h (using namespace std;)
for the Oracle Developer Studio compiler is no longer needed now
C++11 is required so has been removed. A couple more usages of
log() (which should have been std::log()) with an int argument
are reported on Solaris.
* The undocumented limit of 4095 bytes on messages from the
S-compatibility macros PROBLEM and MESSAGE is now documented and
longer messages will be silently truncated rather than
potentially causing segfaults.
* If the R_NO_SEGV_HANDLER environment variable is non-empty, the
signal handler for SEGV/ILL/BUS signals (which offers recovery
user interface) is not set. This allows more reliable debugging
of crashes that involve the console.
DEPRECATED AND DEFUNCT:
* The legacy S-compatibility macros PROBLEM, MESSAGE, ERROR, WARN,
WARNING, RECOVER, ... are deprecated and will be hidden in R
4.2.0. R's native interface of Rf_error and Rf_warning has long
been preferred.
BUG FIXES:
* .mapply(F, dots, .) no longer segfaults when dots is not a list
and uses match.fun(F) as always documented; reported by Andrew
Simmons in PR#18164.
* hist(<Date>, ...) and hist(<POSIXt>, ...) no longer pass
arguments for rect() (such as col and density) to axis().
(Thanks to Sebastian Meyer's PR#18171.)
* \Sexpr{ch} now preserves Encoding(ch). (Thanks to report and
patch by Jeroen Ooms in PR#18152.)
* Setting the RNG to "Marsaglia-Multicarry" e.g., by RNGkind(), now
warns in more places, thanks to Andr'e Gillibert's report and
patch in PR#18168.
* gray(numeric(), alpha=1/2) no longer segfaults, fixing PR#18183,
reported by Till Krenz.
* Fixed dnbinom(x, size=<very_small>, .., log=TRUE) regression,
reported by Martin Morgan.
* as.Date.POSIXlt(x) now keeps names(x), thanks to Davis Vaughan's
report and patch in PR#18188.
* model.response() now strips an "AsIs" class typically, thanks to
Duncan Murdoch's report and other discussants in PR#18190.
* try() is considerably faster in case of an error and long call,
as e.g., from some do.call(). Thanks to Alexander Kaever's
suggestion posted to R-devel.
* qqline(y = <object>) such as y=I(.), now works, see also
PR#18190.
* Non-integer mgp par() settings are now handled correctly in
axis() and mtext(), thanks to Mikael Jagan and Duncan Murdoch's
report and suggestion in PR#18194.
* formatC(x) returns length zero character() now, rather than ""
when x is of length zero, as documented, thanks to Davis
Vaughan's post to R-devel.
* removeSource(fn) now retains (other) attributes(fn).
* Mon Oct 25 2021 Detlef Steuer <detlef.steuer@gmx.de>
- repaired https://bugzilla.suse.com/show_bug.cgi?id=1191380
(rpmacros now go to rpmmacrodir)
- minor clean-ups in spec file
* Tue Aug 10 2021 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.1.1:
NEW FEATURES:
* require(pkg, quietly = TRUE) is quieter and in particular does
not warn if the package is not found.
DEPRECATED AND DEFUNCT:
* Use of ftp:// URIs should be regarded as deprecated, with
on-going support confined to method = "libcurl" and not routinely
tested. (Nowadays no major browser supports them.)
* The non-default method = "internal" is deprecated for http:// and
ftp:// URIs for both download.file and url.
* On Windows, method = "wininet" is deprecated for http://,
https:// and ftp:// URIs for both download.file and url. (A
warning is only given for ftp://.)
For ftp:// URIs the default method is now "libcurl" if available
(which it is on CRAN builds).
method = "wininet" remains the default for http:// and https://
URIs but if libcurl is available, using method = "libcurl" is
preferred.
INSTALLATION:
* make check now works also without a LaTeX installation. (Thanks
to Sebastian Meyer's PR#18103.)
BUG FIXES:
* make check-devel works again in an R build configured with
- -without-recommended-packages.
* qnbinom(p, size, mu) for large size/mu is correct now in a range
of cases (PR#18095); similarly for the (size, prob)
parametrization of the negative binomial. Also qpois() and
qbinom() are better and or faster for extreme cases. The
underlying C code has been modularized and is common to all four
cases of discrete distributions.
* gap.axis is now part of the axis() arguments which are passed
from bxp(), and hence boxplot(). (Thanks to Martin Smith's
report and suggestions in PR#18109.)
* .First and .Last can again be set from the site profile.
* seq.int(from, to, *) and seq.default(..) now work better in large
range cases where from-to is infinite where the two boundaries
are finite.
* all.equal(x,y) now returns TRUE correctly also when several
entries of abs(x) and abs(y) are close to .Machine$double.xmax,
the largest finite numeric.
* model.frame() now clears the object bit when removing the class
attribute of a value via na.action (PR#18100).
* charClass() now works with multi-character strings on Windows
(PR#18104, fixed by Bill Dunlap).
* encodeString() on Solaris now works again in Latin-1 encoding on
characters represented differently in UTF-8. Support for
surrogate pairs on Solaris has been improved.
* file.show() on Windows now works with non-ASCII path names
representable in the current native encoding (PR#18132).
* Embedded R on Windows can now find R home directory via the
registry even when installed only for the current user
(PR#18135).
* pretty(x) with finite x now returns finite values also in the
case where the extreme x values are close in size to the maximal
representable number .Machine$double.xmax.
Also, it's been tweaked for very small ranges and when a boundary
is close (or equal) to zero; e.g., pretty(c(0,1e-317)) no longer
has negative numbers, currently still warning about a very small
range, and pretty(2^-(1024 - 2^-1/(c(24,10)))) is more accurate.
* The error message for not finding vignette files when weaving has
correct file sizes now. (Thanks to Sebastian Meyer's PR#18154.)
* dnbinom(20, <large>, 1) now correctly gives 0, and similar cases
are more accurate with underflow precaution. (Reported by Francisco Vera Alcivar in PR#18072.)
* Fri Jun 04 2021 Detlef Steuer <detlef.steuer@gmx.de>
- The line %{__install} -m 755 -d %{_infodir}
no longer works in TW or Factory.
But without that line it works everywhere. So this instruction
was commented out of the spec file.
* Tue May 18 2021 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.1.0:
FUTURE DIRECTIONS:
* It is planned that the 4.1.x series will be the last to support
32-bit Windows, with production of binary packages for that
series continuing until early 2023.
SIGNIFICANT USER-VISIBLE CHANGES:
* Data set esoph in package datasets now provides the correct
numbers of controls; previously it had the numbers of cases added
to these. (Reported by Alexander Fowler in PR#17964.)
NEW FEATURES:
* www.omegahat.net is no longer one of the repositories known by
default to setRepositories(). (Nowadays it only provides source
packages and is often unavailable.)
* Function package_dependencies() (in package tools) can now use
different dependency types for direct and recursive dependencies.
* The checking of the size of tarball in R CMD check --as-cran
<pkg> may be tweaked via the new environment variable
_R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_, as suggested in
PR#17777 by Jan Gorecki.
* Using c() to combine a factor with other factors now gives a
factor, an ordered factor when combining ordered factors with
identical levels.
* apply() gains a simplify argument to allow disabling of
simplification of results.
* The format() method for class "ftable" gets a new option justify.
(Suggested by Thomas Soeiro.)
* New ...names() utility. (Proposed by Neal Fultz in PR#17705.)
* type.convert() now warns when its as.is argument is not
specified, as the help file always said it _should_. In that
case, the default is changed to TRUE in line with its change in
read.table() (related to stringsAsFactor) in R 4.0.0.
* When printing list arrays, classed objects are now shown _via_
their format() value if this is a short enough character string,
or by giving the first elements of their class vector and their
length.
* capabilities() gets new entry "Rprof" which is TRUE when R has
been configured with the equivalent of --enable-R-profiling (as
it is by default). (Related to Michael Orlitzky's report
PR#17836.)
* str(xS4) now also shows extraneous attributes of an S4 object
xS4.
* Rudimentary support for vi-style tags in rtags() and R CMD rtags
has been added. (Based on a patch from Neal Fultz in PR#17214.)
* checkRdContents() is now exported from tools; it and also
checkDocFiles() have a new option chkInternal allowing to check
Rd files marked with keyword "internal" as well. The latter can
be activated for R CMD check via environment variable
_R_CHECK_RD_INTERNAL_TOO_.
* New functions numToBits() and numToInts() extend the raw
conversion utilities to (double precision) numeric.
* Functions URLencode() and URLdecode() in package utils now work
on vectors of URIs. (Based on patch from Bob Rudis submitted
with PR#17873.)
* path.expand() can expand ~user on most Unix-alikes even when
readline is not in use. It tries harder to expand ~, for example
should environment variable HOME be unset.
* For HTML help (both dynamic and static), Rd file links to help
pages in external packages are now treated as references to
topics rather than file names, and fall back to a file link only
if the topic is not found in the target package. The earlier rule
which prioritized file names over topics can be restored by
setting the environment variable _R_HELP_LINKS_TO_TOPICS_ to a
false value.
* c() now removes NULL arguments before dispatching to methods,
thus simplifying the implementation of c() methods, _but_ for
back compatibility keeps NULL when it is the first argument.
(From a report and patch proposal by Lionel Henry in PR#17900.)
* Vectorize()'s result function's environment no longer keeps
unneeded objects.
* Function ...elt() now propagates visibility consistently with
..n. (Thanks to Lionel Henry's PR#17905.)
* capture.output() no longer uses non-standard evaluation to
evaluate its arguments. This makes evaluation of functions like
parent.frame() more consistent. (Thanks to Lionel Henry's
PR#17907.)
* packBits(bits, type="double") now works as inverse of
numToBits(). (Thanks to Bill Dunlap's proposal in PR#17914.)
* curlGetHeaders() has two new arguments, timeout to specify the
timeout for that call (overriding getOption("timeout")) and TLS
to specify the minimum TLS protocol version to be used for
https:// URIs (_inter alia_ providing a means to check for sites
using deprecated TLS versions 1.0 and 1.1).
* For nls(), an optional constant scaleOffset may be added to the
denominator of the relative offset convergence test for cases
where the fit of a model is expected to be exact, thanks to a
proposal by John Nash. nls(*, trace=TRUE) now also shows the
convergence criterion.
* Numeric differentiation _via_ numericDeriv() gets new optional
arguments eps and central, the latter for taking central divided
differences. The latter can be activated for nls() via
nls.control(nDcentral = TRUE).
* nls() now passes the trace and control arguments to getInitial(),
notably for all self-starting models, so these can also be fit in
zero-noise situations via a scaleOffset. For this reason, the
initial function of a selfStart model must now have ... in its
argument list.
* bquote(splice = TRUE) can now splice expression vectors with
attributes: this makes it possible to splice the result of
parse(keep.source = TRUE). (Report and patch provided by Lionel
Henry in PR#17869.)
* textConnection() gets an optional name argument.
* get(), exists(), and get0() now signal an error if the first
argument has length greater than 1. Previously additional
elements were silently ignored. (Suggested by Antoine Fabri on
R-devel.)
* R now provides a shorthand notation for creating functions, e.g.
\(x) x + 1 is parsed as function(x) x + 1.
* R now provides a simple native forward pipe syntax |>. The
simple form of the forward pipe inserts the left-hand side as the
first argument in the right-hand side call. The pipe
implementation as a syntax transformation was motivated by
suggestions from Jim Hester and Lionel Henry.
* all.equal(f, g) for functions now by default also compares their
environment(.)s, notably via new all.equal method for class
function. Comparison of nls() fits, e.g., may now need
all.equal(m1, m2, check.environment = FALSE).
* .libPaths() gets a new option include.site, allowing to _not_
include the site library. (Thanks to Dario Strbenac's suggestion
and Gabe Becker's PR#18016.)
* Lithuanian translations are now available. (Thanks to Rimantas
Zakauskas.)
* names() now works for DOTSXP objects. On the other hand, in
R-lang, the R language manual, we now warn against relying on the
structure or even existence of such dot-dot-dot objects.
* all.equal() no longer gives an error on DOTSXP objects.
* capabilities("cairo") now applies only to the file-based devices
as it is now possible (if very unusual) to build R with Cairo
support for those but not for X11().
* There is optional support for tracing the progress of
loadNamespace() - see its help.
* (Not Windows.) l10n_info() reports an additional element, the
name of the encoding as reported by the OS (which may differ from
the encoding part (if any) of the result from
Sys.getlocale("LC_CTYPE").
* New function gregexec() which generalizes regexec() to find _all_
disjoint matches and well as all substrings corresponding to
parenthesized subexpressions of the given regular expression.
(Contributed by Brodie Gaslam.)
* New function charClass() in package utils to query the
wide-character classification functions in use (such as
iswprint).
* The names of quantile()'s result no longer depend on the global
getOption("digits"), but quantile() gets a new optional argument
digits = 7 instead.
* grep(), sub(), regexp and variants work considerably faster for
long factors with few levels. (Thanks to Michael Chirico's
PR#18063.)
* Provide grouping of x11() graphics windows within a window
manager such as Gnome or Unity; thanks to a patch by Ivan Krylov
posted to R-devel.
* The split() method for class data.frame now allows the f argument
to be specified as a formula.
* sprintf now warns on arguments unused by the format string.
* New palettes "Rocket" and "Mako" for hcl.colors() (approximating
palettes of the same name from the 'viridisLite' package).
Contributed by Achim Zeileis.
* The base environment and its namespace are now locked (so one can
no longer add bindings to these or remove from these).
* Rterm handling of multi-byte characters has been improved,
allowing use of such characters when supported by the current
locale.
* Rterm now accepts ALT+ +xxxxxxxx sequences to enter Unicode
characters as hex digits.
* Environment variable LC_ALL on Windows now takes precedence over
LC_CTYPE and variables for other supported categories, matching
the POSIX behaviour.
* duplicated() and anyDuplicated() are now optimized for integer
and real vectors that are known to be sorted via the ALTREP
framework. Contributed by Gabriel Becker via PR#17993.
GRAPHICS:
* The graphics engine version, R_GE_version, has been bumped to 14
and so packages that provide graphics devices should be
reinstalled.
* Graphics devices should now specify deviceVersion to indicate
what version of the graphics engine they support.
* Graphics devices can now specify deviceClip. If TRUE, the
graphics engine will never perform any clipping of output itself.
The clipping that the graphics engine does perform (for both
canClip = TRUE and canClip = FALSE) has been improved to avoid
producing unnecessary artifacts in clipped output.
* The grid package now allows gpar(fill) to be a linearGradient(),
a radialGradient(), or a pattern(). The viewport(clip) can now
also be a grob, which defines a clipping path, and there is a new
viewport(mask) that can also be a grob, which defines a mask.
These new features are only supported so far on the Cairo-based
graphics devices and on the pdf() device.
* (Not Windows.) A warning is given when a Cairo-based type is
specified for a png(), jpeg(), tiff() or bmp() device but Cairo
is unsupported (so type = "Xlib" is tried instead).
* grSoftVersion() now reports the versions of FreeType and
FontConfig if they are used directly (not _via_ Pango), as is
most commonly done on macOS.
C-LEVEL FACILITIES:
* The _standalone_ libRmath math library and R's C API now provide
log1pexp() again as documented, and gain log1mexp().
INSTALLATION on a UNIX-ALIKE:
* configure checks for a program pkgconf if program pkg-config is
not found. These are now only looked for on the path (like
almost all other programs) so if needed specify a full path to
the command in PKG_CONFIG, for example in file config.site.
* C99 function iswblank is required - it was last seen missing ca
2003 so the workaround has been removed.
* There are new configure options --with-internal-iswxxxxx,
- -with-internal-towlower and --with-internal-wcwidth which allows
the system functions for wide-character classification,
case-switching and width (wcwidth and wcswidth) to be replaced by
internal ones. The first has long been used on macOS, AIX (and
Windows) but this enables it to be unselected there and selected
for other platforms (it is the new default on Solaris). The
second is new in this version of R and is selected by default on
macOS and Solaris. The third has long been the default and
remains so as it contains customizations for East Asian
languages.
System versions of these functions are often minimally
implemented (sometimes only for ASCII characters) and may not
cover the full range of Unicode points: for example Solaris (and
Windows) only cover the Basic Multilingual Plane.
* Cairo installations without X11 are more likely to be detected by
configure, when the file-based Cairo graphics devices will be
available but not X11(type = "cairo").
* There is a new configure option --with-static-cairo which is the
default on macOS. This should be used when only static cairo
(and where relevant, Pango) libraries are available.
* Cairo-based graphics devices on platforms without Pango but with
FreeType/FontConfig will make use of the latter for font
selection.
LINK-TIME OPTIMIZATION on a UNIX-ALIKE:
* Configuring with flag --enable-lto=R now also uses LTO when
installing the recommended packages.
* R CMD INSTALL and R CMD SHLIB have a new flag --use-LTO to use
LTO when compiling code, for use with R configured with
- -enable-lto=R. For R configured with --enable-lto, they have
the new flag --no-use-LTO.
Packages can opt in or out of LTO compilation _via_ a UseLTO
field in the DESCRIPTION file. (As usual this can be overridden
by the command-line flags.)
BUILDING R on Windows:
* for GCC >= 8, FC_LEN_T is defined in config.h and hence character
lengths are passed from C to Fortran in _inter alia_ BLAS and
LAPACK calls.
* There is a new text file src/gnuwin32/README.compilation, which
outlines how C/Fortran code compilation is organized and
documents new features:
* R can be built with Link-Time Optimization with a suitable
compiler - doing so with GCC 9.2 showed several
inconsistencies which have been corrected.
* There is support for cross-compiling the C and Fortran code
in R and standard packages on suitable (Linux) platforms.
This is mainly intended to allow developers to test later
versions of compilers - for example using GCC 9.2 or 10.x has
detected issues that GCC 8.3 in Rtools40 does not.
* There is experimental support for cross-building R packages
with C, C++ and/or Fortran code.
* The R installer can now be optionally built to support a single
architecture (only 64-bit or only 32-bit).
PACKAGE INSTALLATION:
* The default C++ standard has been changed to C++14 where
available (which it is on all currently checked platforms): if
not (as before) C++11 is used if available otherwise C++ is not
supported.
Packages which specify C++11 will still be installed using C++11.
C++14 compilers may give deprecation warnings, most often for
std::random_shuffle (deprecated in C++14 and removed in C++17).
Either specify C++11 (see 'Writing R Extensions') or modernize
the code and if needed specify C++14. The latter has been
supported since R 3.4.0 so the package's DESCRIPTION would need
to include something like
Depends: R (>= 3.4)
PACKAGE INSTALLATION on Windows:
* R CMD INSTALL and R CMD SHLIB make use of their flag --use-LTO
when the LTO_OPT make macro is set in file etc/${R_ARCH}/Makeconf
or in a personal/site Makevars file. (For details see 'Writing R
Extensions' SS4.5.)
This provides a valuable check on code consistency. It does work
with GCC 8.3 as in Rtools40, but that does not detect everything
the CRAN checks with current GCC do.
PACKAGE INSTALLATION on macOS:
* The default personal library directory on builds with
- -enable-aqua (including CRAN builds) now differs by CPU type,
one of
~/Library/R/x86_64/x.y/library
~/Library/R/arm64/x.y/library
This uses the CPU type R (and hence the packages) were built for,
so when a x86_64 build of R is run under Rosetta emulation on an
arm64 Mac, the first is used.
UTILITIES:
* R CMD check can now scan package functions for bogus return
statements, which were possibly intended as return() calls (wish
of PR#17180, patch by Sebastian Meyer). This check can be
activated via the new environment variable
_R_CHECK_BOGUS_RETURN_, true for --as-cran.
* R CMD build omits tarballs and binaries of previous builds from
the top-level package directory. (PR#17828, patch by Sebastian
Meyer.)
* R CMD check now runs sanity checks on the use of LazyData, for
example that a data directory is present and that
LazyDataCompression is not specified without LazyData and has a
documented value. For packages with large LazyData databases
without specifying LazyDataCompression, there is a reference to
the code given in 'Writing R Extensions' SS1.1.6 to test the
choice of compression (as in all the CRAN packages tested a
non-default method was preferred).
* R CMD build removes LazyData and LazyDataCompression fields from
the DESCRIPTION file of packages without a data directory.
ENCODING-RELATED CHANGES:
* The parser now treats \Unnnnnnnn escapes larger than the upper
limit for Unicode points (\U10FFFF) as an error as they cannot be
represented by valid UTF-8.
Where such escapes are used for outputting non-printable
(including unassigned) characters, 6 hex digits are used (rather
than 8 with leading zeros). For clarity, braces are used, for
example \U{0effff}.
* The parser now looks for non-ASCII spaces on Solaris (as
previously on most other OSes).
* There are warnings (including from the parser) on the use of
unpaired surrogate Unicode points such as \uD834. (These cannot
be converted to valid UTF-8.)
* Functions nchar(), tolower(), toupper() and chartr() and those
using regular expressions have more support for inputs with a
marked Latin-1 encoding.
* The character-classification functions used (by default) to
replace the system iswxxxxx functions on Windows, macOS and AIX
have been updated to Unicode 13.0.0.
The character-width tables have been updated to include new
assignments in Unicode 13.0.0.
* The code for evaluating default (extended) regular expressions
now uses the same character-classification functions as the rest
of R (previously they differed on Windows, macOS and AIX).
* There is a build-time option to replace the system's
wide-character wctrans C function by tables shipped with R: use
configure option --with-internal-towlower or (on Windows)
- DUSE_RI18N_CASE in CFLAGS when building R. This may be needed
to allow tolower() and toupper() to work with Unicode characters
beyond the Basic Multilingual Plane where not supported by system
functions (e.g. on Solaris where it is the new default).
* R is more careful when truncating UTF-8 and other multi-byte
strings that are too long to be printed, passed to the system or
libraries or placed into an internal buffer. Truncation will no
longer produce incomplete multibyte characters.
DEPRECATED AND DEFUNCT:
* Function plclust() from the package stats and
package.dependencies(), pkgDepends(), getDepList(),
installFoundDepends(), and vignetteDepends() from package tools
are defunct.
* Defunct functions checkNEWS() and readNEWS() from package tools
and CRAN.packages() from utils have been removed.
* R CMD config CXXCPP is defunct (it was deprecated in R 3.6.2).
* parallel::detectCores() drops support for Irix (retired in 2013).
* The LINPACK argument to chol.default(), chol2inv(),
solve.default() and svd() has been defunct since R 3.1.0. It was
silently ignored up to R 4.0.3 but now gives an error.
* Subsetting/indexing, such as ddd[*] or ddd$x on a DOTSXP
(dot-dot-dot) object ddd has been disabled; it worked by accident
only and was undocumented.
BUG FIXES:
* Many more C-level allocations (mainly by malloc and strdup) are
checked for success with suitable alternative actions.
* Bug fix for replayPlot(); this was turning off graphics engine
display list recording if a recorded plot was replayed in the
same session. The impact of the bug became visible if resize the
device after replay OR if attempted another savePlot() after
replay (empty display list means empty screen on resize or empty
saved plot).
* R CMD check etc now warn when a package exports non-existing S4
classes or methods, also in case of no "methods" presence.
(Reported by Alex Bertram; reproducible example and patch by
Sebastian Meyer in PR#16662.)
* boxplot() now also accepts calls for labels such as ylab, the
same as plot(). (Reported by Marius Hofert.)
* The help page for xtabs() now correctly states that addNA is
setting na.action = na.pass among others. (Reported as PR#17770
by Thomas Soeiro.)
* The R CMD check <pkg> gives a longer and more comprehensible
message when DESCRIPTION misses dependencies, e.g., in Imports:.
(Thanks to the contributors of PR#17179.)
* update.default() now calls the generic update() on the formula to
work correctly for models with extended formulas. (As reported
and suggested by Neal Fultz in PR#17865.)
* The horizontal position of leaves in a dendrogram is now correct
also with center = FALSE. (PR#14938, patch from Sebastian
Meyer.)
* all.equal.POSIXt() no longer warns about and subsequently ignores
inconsistent "tzone" attributes, but describes the difference in
its return value (PR#17277). This check can be disabled _via_
the new argument check.tzone = FALSE as suggested by Sebastian
Meyer.
* as.POSIXct() now populates the "tzone" attribute from its tz
argument when x is a logical vector consisting entirely of NA
values.
* x[[2^31]] <- v now works. (Thanks to the report and patch by
Suharto Anggono in PR#17330.)
* In log-scale graphics, axis() ticks and label positions are now
computed more carefully and symmetrically in their range,
typically providing _more_ ticks, fulfilling wishes in PR#17936.
The change really corresponds to an improved axisTicks() (package
grDevices), potentially influencing grid and lattice, for
example.
* qnorm(<very large negative>, log.p=TRUE) is now correct to at
least five digits where it was catastrophically wrong,
previously.
* sum(df) and similar "Summary"- and "Math"-group member functions
now work for data frames df with logical columns, notably also of
zero rows. (Reported to R-devel by Martin "b706".)
* unsplit() had trouble with tibbles due to unsound use of rep(NA,
len)-indexing, which should use NA_integer_ (Reported to R-devel
by Mario Annau.)
* pnorm(x, log.p = TRUE) underflows to -Inf slightly later.
* show(<hidden S4 generic>) prints better and without quotes for
non-hidden S4 generics.
* read.table() and relatives treated an "NA" column name as missing
when check.names = FALSE PR#18007.
* Parsing strings containing UTF-16 surrogate pairs such as
"\uD834\uDD1E" works better on some (uncommon) platforms.
sprintf("%X", utf8ToInt("\uD834\uDD1E")) should now give "1D11E"
on all platforms.
* identical(x,y) is no longer true for differing DOTSXP objects,
fixing PR#18032.
* str() now works correctly for DOTSXP and related exotics, even
when these are doomed.
Additionally, it no longer fails for lists with a class and
"irregular" method definitions such that e.g. lapply(*) will
necessarily fail, as currently for different igraph objects.
* Too long lines in environment files (e.g. Renviron) no longer
crash R. This limit has been increased to 100,000 bytes.
(PR#18001.)
* There is a further workaround for FreeType giving incorrect
italic font faces with cairo-based graphics devices on macOS.
* add_datalist(*, force = TRUE) (from package tools) now actually
updates an existing data/datalist file for new content. (Thanks
to a report and patch by Sebastian Meyer in PR#18048.)
* cut.Date() and cut.POSIXt() could produce an empty last interval
for breaks = "months" or breaks = "years". (Reported as PR#18053
by Christopher Carbone.)
* Detection of the encoding of 'regular' macOS locales such as
en_US (which is UTF-8) had been broken by a macOS change:
fortunately these are now rarely used with en_US.UTF-8 being
preferred.
* sub() and gsub(pattern, repl, x, *) now keep attributes of x such
as names() also when pattern is NA (PR#18079).
* Time differences ("difftime" objects) get a replacement and a
rep() method to keep "units" consistent. (Thanks to a report and
patch by Nicolas Bennett in PR#18066.)
* The \RdOpts macro, setting defaults for \Sexpr options in an Rd
file, had been ineffective since R 2.12.0: it now works again.
(Thanks to a report and patch by Sebastian Meyer in PR#18073.)
* mclapply and pvec no longer accidentally terminate parallel
processes started before by mcparallel or related calls in
package parallel (PR#18078).
* grep and other functions for evaluating (extended) regular
expressions handle in Unicode also strings not explicitly flagged
UTF-8, but flagged native when running in UTF-8 locale.
* Fixed a crash in fifo implementation on Windows (PR#18031).
* Binary mode in fifo on Windows is now properly detected from
argument open (PR#15600, PR#18031).
* Tue May 18 2021 Detlef Steuer <detlef.steuer@gmx.de>
- improved spec file according to comments of dimstar in
https://build.opensuse.org/request/show/892685
* Thu May 06 2021 Detlef Steuer <detlef.steuer@gmx.de>
- To get in sync with d:l:R:autoCRAN the Matrix package's split
in -devel was reversed.
* Wed Mar 31 2021 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.0.5:
BUG FIXES:
* The change to the internal table in R 4.0.4 for iswprint has been
reverted: it contained some errors in printability of 'East
Asian' characters.
* For packages using LazyData, R CMD build ignored the
- -resave-data option and the BuildResaveData field of the
DESCRIPTION file (in R versions 4.0.0 to 4.0.4).
* Mon Feb 15 2021 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.0.4:
NEW FEATURES:
* File share/texmf/tex/latex/jss.cls has been updated to work with
LaTeX versions since Oct 2020.
* Unicode character width tables (as used by nchar(, type = "w"))
have been updated to Unicode 12.1 by Brodie Gaslam (PR#17781),
including many emoji.
* The internal table for iswprint (used on Windows, macOS and AIX)
has been updated to include many recent Unicode characters.
INSTALLATION on a UNIX-ALIKE:
* If an external BLAS is specified by --with-blas=foo or _via_
environment variable BLAS_LIBS is not found, this is now a
configuration error. The previous behaviour was not clear from
the documentation: it was to continue the search as if
- -with-blas=yes was specified.
BUG FIXES:
* all.equal(x,y) now "sees" the two different NAs in factors,
thanks to Bill Dunlap and others in PR#17897.
* (~ NULL)[1] and similar formula subsetting now works, thanks to a
report and patch by Henrik Bengtsson in PR#17935. Additionally,
subsetting leaving an empty formula now works too, thanks to
suggestions by Suharto Anggono.
* .traceback(n) keeps source references again, as before R 4.0.0,
fixing a regression; introduced by the PR#17580, reported
including two patch proposals by Brodie Gaslam.
* unlist(plst, recursive=FALSE) no longer drops content for
pairlists with list components, thanks to the report and patch by
Suharto Anggono in PR#17950.
* iconvlist() now also works on MUSL based (Linux) systems, from a
report and patch suggestion by Wesley Chan in PR#17970.
* round() and signif() no longer tolerate wrong argument names,
notably in 1-argument calls; reported by Shane Mueller on R-devel
(mailing list); later reported as PR#17976.
* .Machine has longdouble.* elements only if
capabilities("long.double") is true, as documented. (Previously
they were included if the platform had long double identical to
double, as ARM does.)
* p.adjust(numeric(), n=0) now works, fixing PR#18002.
* identical(x,y) no longer prints "Unknown Type .." for typeof(x)
== "..." objects.
* Fix (auto-)print()ing of named complex vectors, see PR#17868 and
PR#18019.
* all.equal(<language>, <...>) now works, fixing PR#18029.
* as.data.frame.list(L, row.names=NULL) now behaves in line with
data.frame(), disregarding names of components of L, fixing
PR#18034, reported by Kevin Tappe.
* checkRdaFiles(ff)$version is now correct also when ff contains
files of different versions, thanks to a report and patch from
Sebastian Meyer in PR#18041.
* macOS: Quartz device live drawing could fail (no plot is shown)
if the system changes the drawing context after view update
(often the case since macOS Big Sur). System log may show
"CGContextDelegateCreateForContext: invalid context" error.
* Sat Oct 10 2020 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.0.3:
NEW FEATURES:
* On platforms using configure option --with-internal-tzcode,
additional values "internal" and (on macOS only) "macOS" are
accepted for the environment variable TZDIR. (See ?TZDIR.)
On macOS, "macOS" is used by default if the system timezone
database is a newer version than that in the R installation.
* When install.packages(type = "source") fails to find a package in
a repository it mentions package versions which are excluded by
their R version requirement and links to hints on why a package
might not be found.
* The default value for options("timeout") can be set from
enviromnent variable R_DEFAULT_INTERNET_TIMEOUT, still defaulting
to 60 (seconds) if that is not set or invalid.
This may be needed when child R processes are doing downloads,
for example during the installation of source packages which
download jars or other forms of data.
LINK-TIME OPTIMIZATION on a UNIX-ALIKE:
* There is now support for parallelized Link-Time Optimization
(LTO) with GCC and for 'thin' LTO with clang _via_ setting the
LTO macro.
* There is support for setting a different LTO flag for the Fortran
compiler, including to empty when mixing clang and gfortran (as
on macOS). See file config.site.
* There is a new LTO_LD macro to set linker options for LTO
compilation, for example to select an alternative linker or to
parallelize thin LTO.
DEPRECATED AND DEFUNCT:
* The LINPACK argument to chol.default(), chol2inv(),
solve.default() and svd() has been defunct since R 3.1.0. Using
it now gives a warning which will become an error in R 4.1.0.
BUG FIXES:
* The code mitigating stack overflow with PCRE regexps on very long
strings is enabled for PCRE2 < 10.30 also when JIT is enabled,
since stack overflows have been seen in that case.
* Fix to correctly show the group labels in dotchart() (which where
lost in the ylab improvement for R 4.0.0).
* addmargins(*, ..) now also works when fn() is a local function,
thanks to bug report and patch PR#17124 from Alex Bertram.
* rank(x) and hence sort(x) now work when x is an object (as per
is.object(x)) of type "raw" _and_ provides a valid `[` method,
e.g., for gmp::as.bigz(.) numbers.
* chisq.test(*, simulate.p.value=TRUE) and r2dtable() now work
correctly for large table entries (in the millions). Reported by
Sebastian Meyer and investigated by more helpers in PR#16184.
* Low-level socket read/write operations have been fixed to
correctly signal communication errors. Previously, such errors
could lead to a segfault due to invalid memory access. Reported
and debugged by Dmitriy Selivanov in PR#17850.
* quantile(x, pr) works more consistently for pr values slightly
outside [0,1], thanks to Suharto Anggono's PR#17891.
Further, quantile(x, prN, names=FALSE) now works even when prN
contains NAs, thanks to Anggono's PR#17892. Ditto for ordered
factors or Date objects when type = 1 or 3, thanks to PR#17899.
* Libcurl-based internet access, including curlGetHeaders(), was
not respecting the "timeout" option. If this causes
unanticipated timeouts, consider increasing the default by
setting R_DEFAULT_INTERNET_TIMEOUT.
* as.Date(<char>) now also works with an initial "", thanks to
Michael Chirico's PR#17909.
* isS3stdGeneric(f) now detects an S3 generic also when it it is
trace()d, thanks to Gabe Becker's PR#17917.
* R_allocLD() has been fixed to return memory aligned for long
double type PR#16534.
* fisher.test() no longer segfaults when called again after its
internal stack has been exceeded PR#17904.
* Accessing a long vector represented by a compact integer sequence
no longer segfaults (reported and debugged by Hugh Parsonage).
* duplicated() now works also for strings with multiple encodings
inside a single vector PR#17809.
* phyper(11, 15, 0, 12, log.p=TRUE) no longer gives NaN; reported
as PR#17271 by Alexey Stukalov.
* Fix incorrect calculation in logLik.nls() PR#16100, patch from
Sebastian Meyer.
* A very old bug could cause a segfault in model.matrix() when
terms involved logical variables. Part of PR#17879.
* model.frame.default() allowed data = 1, leading to involuntary
variable capture (rest of PR#17879).
* tar() no longer skips non-directory files, thanks to a patch by
Sebastian Meyer, fixing the remaining part of PR#16716.
* Mon Jun 22 2020 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.0.2:
UTILITIES:
* R CMD check skips vignette re-building (with a warning) if the
VignetteBuilder package(s) are not available.
BUG FIXES:
* Paths with non-ASCII characters caused problems for package
loading on Windows PR#17833.
* Using tcltk widgets no longer crashes R on Windows.
* source(*, echo=TRUE) no longer fails in some cases with empty
lines; reported by Bill Dunlap in PR#17769.
* on.exit() now correctly matches named arguments, thanks to
PR#17815 (including patch) by Brodie Gaslam.
* regexpr(*, perl=TRUE) no longer returns incorrect positions into
text containing characters outside of the Unicode Basic
Multilingual Plane on Windows.
* Sat Jun 06 2020 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.0.1:
NEW FEATURES:
* paste() and paste0() gain a new optional argument recycle0. When
set to true, zero-length arguments are recycled leading to
character(0) after the sep-concatenation, i.e., to the empty
string "" if collapse is a string and to the zero-length value
character(0) when collapse = NULL.
A package whose code uses this should depend on R (>= 4.0.1).
* The summary(<warnings>) method now maps the counts correctly to
the warning messages.
BUG FIXES:
* aov(frml, ...) now also works where the formula deparses to more
than 500 characters, thanks to a report and patch proposal by Jan
Hauffa.
* Fix a dozen places (code, examples) as Sys.setlocale() returns
the new rather than the previous setting.
* Fix for adding two complex grid units via sum(). Thanks to Gu
Zuguang for the report and Thomas Lin Pedersen for the patch.
* Fix parallel::mclapply(..., mc.preschedule=FALSE) to handle raw
vector results correctly. PR#17779
* Computing the base value, i.e., 2, "everywhere", now uses
FLT_RADIX, as the original machar code looped indefinitely on the
ppc64 architecture for the longdouble case.
* In R 4.0.0, sort.list(x) when is.object(x) was true, e.g., for x
<- I(letters), was accidentally using method = "radix".
Consequently, e.g., merge(<data.frame>) was much slower than
previously; reported in PR#17794.
* plot(y ~ x, ylab = quote(y[i])) now works, as e.g., for xlab;
related to PR#10525.
* parallel::detect.cores(all.tests = TRUE) tries a matching OS name
before the other tests (which were intended only for unknown
OSes).
* Parse data for raw strings is now recorded correctly. Reported by
Gabor Csardi.
* Fri Apr 24 2020 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN 4.0.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* Packages need to be (re-)installed under this version (4.0.0) of
R.
* matrix objects now also inherit from class "array", so e.g.,
class(diag(1)) is c("matrix", "array"). This invalidates code
incorrectly assuming that class(matrix_obj)) has length one.
S3 methods for class "array" are now dispatched for matrix
objects.
* There is a new syntax for specifying _raw_ character constants
similar to the one used in C++: r"(...)" with ... any character
sequence not containing the sequence )". This makes it easier to
write strings that contain backslashes or both single and double
quotes. For more details see ?Quotes.
* R now uses a stringsAsFactors = FALSE default, and hence by
default no longer converts strings to factors in calls to
data.frame() and read.table().
A large number of packages relied on the previous behaviour and
so have needed/will need updating.
* The plot() S3 generic function is now in package base rather than
package graphics, as it is reasonable to have methods that do not
use the graphics package. The generic is currently re-exported
from the graphics namespace to allow packages importing it from
there to continue working, but this may change in future.
Packages which define S4 generics for plot() should be
re-installed and package code using such generics from other
packages needs to ensure that they are imported rather than rely
on their being looked for on the search path (as in a namespace,
the base namespace has precedence over the search path).
REFERENCE COUNTING:
* Reference counting is now used instead of the NAMED mechanism for
determining when objects can be safely mutated in base C code.
This reduces the need for copying in some cases and should allow
further optimizations in the future. It should help make the
internal code easier to maintain.
This change is expected to have almost no impact on packages
using supported coding practices in their C/C++ code.
MIGRATION TO PCRE2:
* This version of R is built against the PCRE2 library for
Perl-like regular expressions, if available. (On non-Windows
platforms PCRE1 can optionally be used if PCRE2 is not available
at build time.) The version of PCRE in use can be obtained _via_
extSoftVersion(): PCRE1 (formerly known as 'PCRE') has versions
<= 8, PCRE2 versions >= 10.
* Making PCRE2 available when building R from source is strongly
recommended (preferably version 10.30 or later) as PCRE1 is no
longer developed: version 8.44 is 'likely to be the final
release'.
* PCRE2 reports errors for some regular expressions that were
accepted by PCRE1. A hyphen now has to be escaped in a character
class to be interpreted as a literal (unless first or last in the
class definition). \R, \B and \X are no longer allowed in
character classes (PCRE1 treated these as literals).
* Option PCRE_study is no longer used with PCRE2, and is reported
as FALSE when that is in use.
NEW FEATURES:
* assertError() and assertWarning() (in package tools) can now
check for _specific_ error or warning classes _via_ the new
optional second argument classes (which is not back compatible
with previous use of an unnamed second argument).
* DF2formula(), the utility for the data frame method of formula(),
now works without parsing and explicit evaluation, starting from
Suharto Anggono's suggestion in PR#17555.
* approxfun() and approx() gain a new argument na.rm defaulting to
true. If set to false, missing y values now propagate into the
interpolated values.
* Long vectors are now supported as the seq argument of a for()
loop.
* str(x) gets a new deparse.lines option with a default to speed it
up when x is a large call object.
* The internal traceback object produced when an error is signalled
(.Traceback), now contains the calls rather than the _deparse()d_
calls, deferring the deparsing to the user-level functions
.traceback() and traceback(). This fulfils the wish of PR#17580,
reported including two patch proposals by Brodie Gaslam.
* data.matrix() now converts character columns to factors and from
this to integers.
* package.skeleton() now explicitly lists all exports in the
NAMESPACE file.
* New function .S3method() to register S3 methods in R scripts.
* file.path() has some support for file paths not in the session
encoding, e.g. with UTF-8 inputs in a non-UTF-8 locale the output
is marked as UTF-8.
* Most functions with file-path inputs will give an explicit error
if a file-path input in a marked encoding cannot be translated
(to the native encoding or in some cases on Windows to UTF-8),
rather than translate to a different file path using escapes.
Some (such as dir.exists(), file.exists(), file.access(),
file.info(), list.files(), normalizePath() and path.expand())
treat this like any other non-existent file, often with a
warning.
* There is a new help document accessed by help("file path
encoding") detailing how file paths with marked encodings are
handled.
* New function list2DF() for creating data frames from lists of
variables.
* iconv() has a new option sub = "Unicode" to translate UTF-8 input
invalid in the to encoding using <U+xxxx> escapes.
* There is a new function infoRDS() providing information about the
serialization format of a serialized object.
* S3 method lookup now by default skips the elements of the search
path between the global and base environments.
* Added an argument add_datalist(*, small.size = 0) to allow the
creation of a data/datalist file even when the total size of the
data sets is small.
* The backquote function bquote() has a new argument splice to
enable splicing a computed list of values into an expression,
like ,@ in LISP's backquote.
* The formula interface to t.test() and wilcox.test() has been
extended to handle one-sample and paired tests.
* The palette() function has a new default set of colours (which
are less saturated and have better accessibility properties).
There are also some new built-in palettes, which are listed by
the new palette.pals() function. These include the old default
palette under the name "R3". Finally, the new palette.colors()
function allows a subset of colours to be selected from any of
the built-in palettes.
* n2mfrow() gains an option asp = 1 to specify the aspect ratio,
fulfilling the wish and extending the proposal of Michael Chirico
in PR#17648.
* For head(x, n) and tail() the default and other S3 methods
notably for _vector_ n, e.g. to get a "corner" of a matrix, has
been extended to array's of higher dimension thanks to the patch
proposal by Gabe Becker in PR#17652. Consequently, optional
argument addrownums is deprecated and replaced by the (more
general) argument keepnums. An invalid second argument n now
leads to typically more easily readable error messages.
* New function .class2() provides the full character vector of
class names used for S3 method dispatch.
* Printing methods(..) now uses a new format() method.
* sort.list(x) now works for non-atomic objects x and method =
"auto" (the default) or "radix" in cases order(x) works.
* Where they are available, writeBin() allows long vectors.
* New function deparse1() produces one string, wrapping deparse(),
to be used typically in deparse1(substitute(*)), e.g., to fix
PR#17671.
* wilcox.test() enhancements: In the (non-paired) two-sample case,
Inf values are treated as very large for robustness consistency.
If exact computations are used, the result now has "exact" in the
method element of its return value. New arguments tol.root and
digits.rank where the latter may be used for stability to treat
very close numbers as ties.
* readBin() and writeBin() now report an error for an invalid
endian value. The affected code needs to be fixed with care as
the old undocumented behavior was to swap endian-ness in such
cases.
* sequence() is now an S3 generic with an internally implemented
default method, and gains arguments to generate more complex
sequences. Based on code from the S4Vectors Bioconductor package
and the advice of Herv'e Pag`es.
* print()'s default method and many other methods (by calling the
default eventually and passing ...) now make use of a new
optional width argument, avoiding the need for the user to set
and reset options("width").
* memDecompress() supports the RFC 1952 format (e.g. in-memory
copies of gzip-compressed files) as well as RFC 1950.
* memCompress() and memDecompress() support long raw vectors for
types "gzip" and "zx".
* sweep() and slice.index() can now use names of dimnames for their
MARGIN argument (apply has had this for almost a decade).
* New function proportions() and marginSums(). These should replace
the unfortunately named prop.table() and margin.table(). They are
drop-in replacements, but also add named-margin functionality.
The old function names are retained as aliases for
back-compatibility.
* Functions rbinom(), rgeom(), rhyper(), rpois(), rnbinom(),
rsignrank() and rwilcox() which have returned integer since R
3.0.0 and hence NA when the numbers would have been outside the
integer range, now return double vectors (without NAs, typically)
in these cases.
* matplot(x,y) (and hence matlines() and matpoints()) now call the
corresponding methods of plot() and lines(), e.g, when x is a
"Date" or "POSIXct" object; prompted by Spencer Graves'
suggestion.
* stopifnot() now allows customizing error messages via argument
names, thanks to a patch proposal by Neal Fultz in PR#17688.
* unlink() gains a new argument expand to disable wildcard and
tilde expansion. Elements of x of value "~" are now ignored.
* mle() in the stats4 package has had its interface extended so
that arguments to the negative log-likelihood function can be one
or more vectors, with similar conventions applying to bounds,
start values, and parameter values to be kept fixed. This
required a minor extension to class "mle", so saved objects from
earlier versions may need to be recomputed.
* The default for pdf() is now useDingbats = FALSE.
* The default fill colour for hist() and boxplot() is now col =
"lightgray".
* The default order of the levels on the y-axis for spineplot() and
cdplot() has been reversed.
* If the R_ALWAYS_INSTALL_TESTS environment variable is set to a
true value, R CMD INSTALL behaves as if the --install-tests
option is always specified. Thanks to Reinhold Koch for the
suggestion.
* New function R_user_dir() in package tools suggests paths
appropriate for storing R-related user-specific data,
configuration and cache files.
* capabilities() gains a new logical option Xchk to avoid warnings
about X11-related capabilities.
* The internal implementation of grid units has changed, but the
only visible effects at user-level should be
* a slightly different print format for some units (especially
unit arithmetic),
* faster performance (for unit operations) and
* two new functions unitType() and unit.psum().
Based on code contributed by Thomas Lin Pedersen.
* When internal dispatch for rep.int() and rep_len() fails, there
is an attempt to dispatch on the equivalent call to rep().
* Object .Machine now contains new longdouble.* entries (when R
uses long doubles internally).
* news() has been enhanced to cover the news on R 3.x and 2.x.
* For consistency, N <- NULL; N[[1]] <- val now turns N into a list
also when val) has length one. This enables dimnames(r1)[[1]] <-
"R1" for a 1-row matrix r1, fixing PR#17719 reported by Serguei
Sokol.
* deparse(..), dump(..), and dput(x, control = "all") now include
control option "digits17" which typically ensures 1:1
invertibility. New option control = "exact" ensures numeric
exact invertibility via "hexDigits".
* When loading data sets via read.table(), data() now uses
LC_COLLATE=C to ensure locale-independent results for possible
string-to-factor conversions.
* A server socket connection, a new connection type representing a
listening server socket, is created via serverSocket() and can
accept multiple socket connections via socketAccept().
* New function socketTimeout() changes the connection timeout of a
socket connection.
* The time needed to start a homogeneous PSOCK cluster on localhost
with many nodes has been significantly reduced (package
parallel).
* New globalCallingHandlers() function to establish global
condition handlers. This allows registering default handlers for
specific condition classes. Developed in collaboration with
Lionel Henry.
* New function tryInvokeRestart() to invoke a specified restart if
one is available and return without signaling an error if no such
restart is found. Contributed by Lionel Henry in PR#17598.
* str(x) now shows the length of attributes in some cases for a
data frame x.
* Rprof() gains a new argument filter.callframes to request that
intervening call frames due to lazy evaluation or explicit eval()
calls be omitted from the recorded profile data. Contributed by
Lionel Henry in PR#17595.
* The handling of ${FOO-bar} and ${FOO:-bar} in Renviron files now
follows POSIX shells (at least on a Unix-alike), so the first
treats empty environment variables as set and the second does
not. Previously both ignored empty variables. There are several
uses of the first form in etc/Renviron.
* New classes argument for suppressWarnings() and
suppressMessages() to selectively suppress only warnings or
messages that inherit from particular classes. Based on patch
from Lionel Henry submitted with PR#17619.
* New function activeBindingFunction() retrieves the function of an
active binding.
* New "cairoFT" and "pango" components in the output of
grSoftVersion().
* New argument symbolfamily in cairo-based graphics devices and new
function cairoSymbolFont() that can be used to provide the value
for that argument.
Windows:
* Rterm now works also when invoked from MSYS2 terminals. Line
editing is possible when command winpty is installed.
* normalizePath() now resolves symbolic links and normalizes case
of long names of path elements in case-insensitive folders
(PR#17165).
* md5sum() supports UTF-8 file names with characters that cannot be
translated to the native encoding (PR#17633).
* Rterm gains a new option --workspace to specify the workspace to
be restored. This allows equals to be part of the name when
opening _via_ Windows file associations (reported by Christian
Asseburg).
* Rterm now accepts ALT+xxx sequences also with NumLock on. Tilde
can be pasted with an Italian keyboard (PR#17679).
* R falls back to copying when junction creation fails during
package checking (patch from Duncan Murdoch).
DEPRECATED AND DEFUNCT:
* Make macro F77_VISIBILITY has been removed and replaced by
F_VISIBILITY.
* Make macros F77, FCPIFCPLAGS and SHLIB_OPENMP_FCFLAGS have been
removed and replaced by FC, FPICFLAGS and SHLIB_OPENMP_FFLAGS
respectively. (Most make programs will set F77 to the value of
FC, which is set for package compilation. But portable code
should not rely on this.)
* The deprecated support for specifying C++98 for package
installation has been removed.
* R CMD config no longer knows about the unused settings F77 and
FCPIFCPLAGS, nor CXX98 and similar.
* Either PCRE2 or PCRE1 >= 8.32 (Nov 2012) is required: the
deprecated provision for 8.20-8.31 has been removed.
* Defunct functions mem.limits(), .readRDS(),
.saveRDS(),..find.package(), and .path.package() from package
base and allGenerics(), getAccess(), getAllMethods(),
getClassName(), getClassPackage(), getExtends(), getProperties(),
getPrototype(), getSubclasses(), getVirtual(), mlistMetaName(),
removeMethodsObject(), seemsS4Object(), traceOff(), and traceOn()
from methods have been removed.
C-LEVEL FACILITIES:
* installChar is now remapped in Rinternals.h to installTrChar, of
which it has been a wrapper since R 3.6.0. Neither are part of
the API, but packages using installChar can replace it if they
depend on R >= 3.6.2.
* Header R_ext/Print.h defines R_USE_C99_IN_CXX and hence exposes
Rvprintf and REvprintf if used with a C++11 (or later) compiler.
* There are new Fortran subroutines dblepr1, realpr1 and intpr1 to
print a scalar variable (gfortran 10 enforces the distinction
between scalars and length-one arrays). Also labelpr to print
just a label.
* R_withCallingErrorHandler is now available for establishing a
calling handler in C code for conditions inheriting from class
error.
INSTALLATION on a UNIX-ALIKE:
* User-set DEFS (e.g., in config.site) is now used for compiling
packages (including base packages).
* There is a new variant option --enable-lto=check for checking
consistency of BLAS/LAPACK/LINPACK calls - see 'Writing R
Extensions'.
* A C++ compiler default is set only if the C++11 standard is
supported: it no longer falls back to C++98.
* PCRE2 is used if available. To make use of PCRE1 if PCRE2 is
unavailable, configure with option --with-pcre1.
* The minimum required version of libcurl is now 7.28.0 (Oct 2012).
* New make target distcheck checks
* R can be rebuilt from the tarball created by make dist,
* the build from the tarball passes make check-all,
* the build installs and uninstalls,
* the source files are properly cleaned by make distclean.
UTILITIES:
* R --help now mentions the option --no-echo (renamed from --slave)
and its previously undocumented short form -s.
* R CMD check now optionally checks configure and cleanup scripts
for non-Bourne-shell code ('bashisms').
* R CMD check --as-cran now runs \donttest examples (which are run
by example()) instead of instructing the tester to do so. This
can be temporarily circumvented during development by setting
environment variable _R_CHECK_DONTTEST_EXAMPLES_ to a false
value.
PACKAGE INSTALLATION:
* There is the beginnings of support for the recently approved
C++20 standard, specified analogously to C++14 and C++17. There
is currently only limited support for this in compilers, with
flags such as -std=c++20 and -std=c++2a. For the time being the
configure test is of accepting one of these flags and compiling
C++17 code.
BUG FIXES:
* formula(x) with length(x) > 1 character vectors, is deprecated
now. Such use has been rare, and has 'worked' as expected in
some cases only. In other cases, wrong x have silently been
truncated, not detecting previous errors.
* Long-standing issue where the X11 device could lose events
shortly after startup has been addressed (PR#16702).
* The data.frame method for rbind() no longer drops <NA> levels
from factor columns by default (PR#17562).
* available.packages() and hence install.packages() now pass their
... argument to download.file(), fulfilling the wish of PR#17532;
subsequently, available.packages() gets new argument quiet,
solving PR#17573.
* stopifnot() gets new argument exprObject to allow an R object of
class expression (or other 'language') to work more consistently,
thanks to suggestions by Suharto Anggono.
* conformMethod() now works correctly in cases containing a "&&
logic" bug, reported by Henrik Bengtsson. It now creates methods
with "missing" entries in the signature. Consequently,
rematchDefinition() is amended to use appropriate .local() calls
with named arguments where needed.
* format.default(*, scientific = FALSE) now corresponds to a
practically most extreme options(scipen = n) setting rather than
arbitrary n = 100.
* format(as.symbol("foo")) now works (returning "foo").
* postscript(.., title = *) now signals an error when the title
string contains a character which would produce corrupt
PostScript, thanks to PR#17607 by Daisuko Ogawa.
* Certain Ops (notably comparison such as ==) now also work for
0-length data frames, after reports by Hilmar Berger.
* methods(class = class(glm(..))) now warns more usefully and only
once.
* write.dcf() no longer mangles field names (PR#17589).
* Primitive replacement functions no longer mutate a referenced
first argument when used outside of a complex assignment context.
* A better error message for contour(*, levels = Inf).
* The return value of contourLines() is no longer invisible().
* The Fortran code for calculating the coefficients component in
lm.influence() was very inefficient. It has (for now) been
replaced with much faster R code (PR#17624).
* cm.colors(n) _etc_ no longer append the code for alpha = 1, "FF",
to all colors. Hence all eight *.colors() functions and
rainbow() behave consistently and have the same non-explicit
default (PR#17659).
* dnorm had a problematic corner case with sd == -Inf or negative
sd which was not flagged as an error in all cases. Thanks to
Stephen D. Weigand for reporting and Wang Jiefei for analyzing
this; similar change has been made in dlnorm().
* The optional iter.smooth argument of plot.lm(), (the plot()
method for lm and glm fits) now defaults to 0 for all glm fits.
Especially for binary observations with high or low fitted
probabilities, this effectively deleted all observations of 1 or
0. Also, the type of residuals used in the glm case has been
switched to "pearson" since deviance residuals do not in general
have approximately zero mean.
* In plot.lm, Cook's distance was computed from unweighted
residuals, leading to inconsistencies. Replaced with usual
weighted version. (PR#16056)
* Time-series ts(*, start, end, frequency) with fractional
frequency are supported more consistently; thanks to a report
from Johann Kleinbub and analysis and patch by Duncan Murdoch in
PR#17669.
* In case of errors mcmapply() now preserves attributes of returned
"try-error" objects and avoids simplification, overriding
SIMPLIFY to FALSE. (PR#17653)
* as.difftime() gets new optional tz = "UTC" argument which should
fix behaviour during daylight-savings-changeover days, fixing
PR#16764, thanks to proposals and analysis by Johannes Ranke and
Kirill M"uller.
* round() does a better job of rounding _"to nearest"_ by
_measuring_ and _"to even"_; thanks to a careful algorithm
originally prompted by the report from Adam Wheeler and then
others, in PR#17668.
round(x, dig) for _negative_ digits is much more rational now,
notably for large |dig|.
* Inheritance information on S4 classes is maintained more
consistently, particularly in the case of class unions (in part
due to PR#17596 and a report from Ezra Tucker).
* is() behaves more robustly when its argument class2 is a
classRepresentation object.
* The warning message when attempting to export an nonexistent
class is now more readable; thanks to Thierry Onkelinx for
recognizing the problem.
* choose() misbehaved in corner cases where it switched n - k for k
and n was only _nearly_ integer (report from Erik Scott Wright).
* mle() in the stats4 package had problems combining use of box
constraints and fixed starting values (in particular, confidence
intervals were affected).
* Operator ? now has lower precedence than = to work as documented,
so = behaves like <- in help expressions (PR#16710).
* smoothEnds(x) now returns integer type in _both_ cases when x is
integer, thanks to a report and proposal by Bill Dunlap PR#17693.
* The methods package does a better job of tracking inheritance
relationships across packages.
* norm(diag(c(1, NA)), "2") now works.
* subset() had problems with 0-col dataframes (reported by Bill
Dunlap, PR#17721).
* Several cases of integer overflow detected by the 'undefined
behaviour sanitizer' of clang 10 have been circumvented. One in
rhyper() may change the generated value for large input values.
* dotchart() now places the y-axis label (ylab) much better, not
overplotting labels, thanks to a report and suggestion by Alexey
Shipunov.
* A rare C-level array overflow in chull() has been worked around.
* Some invalid specifications of the day-of-the-year (_via_ %j,
e.g. day 366 in 2017) or week plus day-of-the-week are now
detected by strptime(). They now return NA but give a warning as
they may have given random results or corrupted memory in earlier
versions of R.
* socketConnection(server = FALSE) now respects the connection
timeout also on Linux.
* socketConnection(server = FALSE) no longer leaks a connection
that is available right away without waiting (e.g. on localhost).
* Socket connections are now robust against spurious readability
and spurious availability of an incoming connection.
* blocking = FALSE is now respected also on the server side of a
socket connection, allowing non-blocking read operations.
* anova.glm() and anova.glmlist() computed incorrect score (Rao)
tests in no-intercept cases. (Andr'e Gillibert, PR#17734)
* summaryRprof() now should work correctly for the Rprof(*,
memory.profiling=TRUE) case with small chunk size (and "tseries"
or similar) thanks to a patch proposal by Benjamin Tyner, in
PR#15886.
* xgettext() ignores strings passed to ngettext(), since the latter
is handled by xngettext(). Thanks to Daniele Medri for the report
and all the recent work he has done on the Italian translations.
* data(package = "P") for P in base and stats no longer reports the
data sets from package datasets (which it did for back
compatibility for 16 years), fixing PR#17730.
* x[[Inf]] (returning NULL) no longer leads to undefined behavior,
thanks to a report by Kirill M"uller in PR#17756. Further,
x[[-Inf]] and x[[-n]] now give more helpful error messages.
* Gamma() family sometimes had trouble storing link name PR#15891
BUG FIXES (Windows):
* Sys.glob() now supports all characters from the Unicode Basic
Multilingual Plane, no longer corrupting some (less commonly
used) characters (PR#17638).
* Rterm now correctly displays multi-byte-coded characters
representable in the current native encoding (at least on Windows
10 they were sometimes omitted, PR#17632).
* scan() issues with UTF-8 data when running in a DBCS locale have
been resolved (PR#16520, PR#16584).
* RTerm now accepts enhanced/arrow keys also with ConPTY.
* R can can now be started _via_ the launcher icon in a user
documents directory whose path is not representable in the system
encoding.
* socketConnection(server = FALSE) now returns instantly also on
Windows when connection failure is signalled.
* Problems with UTF-16 surrogate pairs have been fixed in several
functions, including tolower() and toupper() (PR#17645).
* Sat Feb 29 2020 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 3.6.3:
NEW FEATURES:
* The included LAPACK has been updated to version 3.9.0 (for the
included routines, just bug fixes).
BUG FIXES:
* Fixed a C level integer overflow in rhyper(); reported by
Benjamin Tyner in PR#17694.
* Uses of url(gzcon(.)) needing to extend buffer size have failed
(with HTTP/2 servers), reported by G'abor Cs'ardi.
* predict(loess(..), se=TRUE) now errors out (instead of
seg.faulting etc) for large sample sizes, thanks to a report and
patch by Benjamin Tyner in PR#17121.
* tools:assertCondition(., "error") and hence assertError() no
longer return errors twice (invisibly).
* update(form, new) in the case of a long new formula sometimes
wrongly eliminated the intercept from form, or (more rarely)
added a garbage term (or seg.faulted !); the fix happened by
simplifying the C-level logic of terms.formula(). Reported by
Mathias Amb"uhl in PR#16326.
* The error message from stopifnot(.., <error producing call>)
again contains the full "stopifnot(.......)" call: Its attempted
suppression did not work consistently.
* On Windows, download.file(., , "wininet", headers=character())
would fail; reported with patch proposal by Kevin Ushey in
PR#17710.
* Mon Jan 20 2020 Dan Čermák <dcermak@suse.com>
- Don't mark %{_libdir}/R/doc as %doc:
This causes issues for rstudio, which requires the directory %{_libdir}/R/doc
to exist, but the directory is not present if libzypp is configured to omit
documentation.
* Thu Dec 12 2019 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 3.6.2:
NEW FEATURES:
* runmed(x, *) gains a new option na.action determining _how_ to
handle NaN or NA in x.
* dotchart() gains new options ann, xaxt, frame.plot and log.
INSTALLATION on a UNIX-ALIKE:
* Detection of the C stack direction has been moved from run-time
to configure: this is safer with LTO builds and allows the
detection to be overridden - see file config.site.
* Source-code changes enable installation on platforms using gcc
- fno-common (the expected default for gcc 10.x).
C-LEVEL FACILITIES:
* installTrChar (which is nowadays is wrapped by installChar) is
defined in Rinternals.h. (Neither are part of the API.)
PACKAGE INSTALLATION:
* Header Rconfig.h contains the value of FC_LEN_T deduced at
installation which is used by the prototypes in headers
R_ext/BLAS.h and R_ext/Lapack.h but to avoid extensive breakage
this is only exposed when USE_FC_LEN_T is defined.
If a package's C/C++ calls to BLAS/LAPACK allow for the 'hidden'
arguments used by most Fortran compilers to pass the lengths of
Fortran character arguments, define USE_FC_LEN_T and include
Rconfig.h (possibly _via_ R.h) before including R_ext/BLAS.h or
R_ext/Lapack.h.
* A package with Fortran source code and perhaps C (but not C++)
sources can request for its shared object/DLL to be linked by the
Fortran compiler by including a line USE_FC_TO_LINK= in
src/Makevars[.win] and using $(SHLIB_OPENMP_FFLAGS) as part of
PKG_LIBS.
The known reason for doing so is a package which uses Fortran
(only) OpenMP on a platform where the Fortran OpenMP runtime is
incompatible with the C one (e.g. gfortran 9.x with clang).
UTILITIES:
* R CMD check has a new option to mitigate checks leaving
files/directories in /tmp. See the 'R Internals' manual - this
is part of --as-cran.
Windows:
* The default standard for C++ in package installation is C++11 (as
it has been on other platforms where available since R 3.6.0: the
default toolchain on Windows was defaulting to C++98).
DEPRECATED AND DEFUNCT:
* Support for specifying C++98 in package installation is
deprecated.
* Support in R CMD config for F77, FCPIFCPLAGS, CPP, CXXCPP and
CXX98 and similar is deprecated. (CPP is found from the system
make and may well not be set.)
Use $CC -E and $CXX -E instead of CPP and CXXCPP.
BUG FIXES:
* runmed(x, *) when x contains missing values now works
consistently for both algorithm="Stuetzle" and "Turlach", and no
longer segfaults for "Turlach", as reported by Hilmar Berger.
* apply(diag(3), 2:3, mean) now gives a helpful error message.
* dgamma(x, shape, log=TRUE) now longer overflows to Inf for shape
< 1 and very small x, fixing PR#17577, reported by Jonathan
Rougier.
* Buffer overflow in building error messages fixed. Reported by
Benjamin Tremblay.
* options(str = .) is correctly initialized at package utils load
time, now. A consequence is that str() in scripts now is more
consistent to interactive use, e.g., when displaying function(**)
argument lists.
* as.numeric(<call>) now gives correct error message.
* Printing ls.str() no longer wrongly shows "<missing>" in rare
cases.
* Auto-printing S4 objects no longer duplicates the object, for
faster speed and reduced memory consumption. Reported by Aaron
Lun.
* pchisq(<LRG>, <LRG>, ncp=100) no longer takes practically forever
in some cases. Hence ditto for corresponding qchisq() calls.
* x %% L for finite x no longer returns NaN when L is infinite, nor
suffers from cancellation for large finite L, thanks to Long Qu's
PR#17611.
Analogously, x %/% L and L %/% x suffer less from cancellation
and return values corresponding to limits for large L.
* grepl(NA, *) now returns logical as documented.
* options(warn=1e11) is an error now, instead of later leading to C
stack overflow because of infinite recursion.
* R_tryCatch no longer transfers control for all conditions.
Reported and patch provided by Lionel Henry in PR#17617.
* format(object.size(.), digits=NULL) now works, fixing PR#17628
reported by Jonathan Carroll.
* get_all_vars(f, d) now also works for cases, e.g. where d
contains a matrix. Reported by Simon Wood in 2009 and patch
provided by Ben Bolker in PR#13624.
Additionally, it now also works when some variables are data
frames, fixing PR#14905, reported by Patrick Breheny.
* barplot() could get spacings wrong if there were exactly two bars
PR#15522. Patch by Michael Chirico.
* power.t.test() works in more cases when returning values of n
smaller than 2.
* dotchart(*, pch=., groups=.) now works better. Reported by
Robert and confirmed by Nic Rochette in PR#16953.
* canCoerce(obj, cl) no longer assumes length(class(obj)) == 1.
* plot.formula(*, subset = *) now also works in a boundary case
reported by Robert Schlicht (TU Dresden).
* readBin() and writeBin() of a rawConnection() now also work in
large cases, thanks to a report and proposal by Taeke Harkema in
PR#17665.
* Thu Oct 17 2019 Richard Brown <rbrown@suse.com>
- Remove obsolete Groups tag (fate#326485)
* Fri Aug 30 2019 John Vandenberg <jayvdb@gmail.com>
- Use %license
* Sun Aug 11 2019 John Vandenberg <jayvdb@gmail.com>
- Fix Summary of R-core and R-core-devel
* Fri Jul 05 2019 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 3.6.1:
INSTALLATION on a UNIX-ALIKE:
* The default detection of the shell variable libNN is overridden
for derivatives of Debian Linux, some of which have started to
have a /usr/lib64 directory. (E.g. Ubuntu 19.04.) As before, it
can be specified in config.site.
UTILITIES:
* R CMD config knows the values of AR and RANLIB, often set for LTO
builds.
DEPRECATED AND DEFUNCT:
* The use of a character vector with .Fortran() is formally
deprecated and gives a non-portability warning. (It has long
been strongly discouraged in 'Writing R Extensions'.)
BUG FIXES:
* On Windows, GUI package installation via menuInstallPkgs() works
again, thanks to Len Weil's and Duncan Murdoch's PR#17556.
* R CMD check on data() fixing PR#17558 thanks to Duncan Murdoch.
* quasi(*, variance = list(..)) now works more efficiently, and
should work in all cases fixing PR#17560. Further, quasi(var =
mu(1-mu)) and quasi(var = "mu ^ 3") now work, and quasi(variance
= "log(mu)") now gives a correct error message.
* Creation of lazy loading database during package installation is
again robust to Rprofile changing the current working directory
(PR#17559).
* boxplot(y ~ f, horizontal=TRUE) now produces correct x- and
y-labels.
* rbind.data.frame() allows to keep <NA> levels from factor columns
(PR#17562) via new option factor.exclude.
Additionally, it works in one more case with matrix-columns which
had been reported on 2017-01-16 by Krzysztof Banas.
* Correct messaging in C++ pragma checks in tools code for R CMD
check, fixing PR#17566 thanks to Xavier Robin.
* print()ing and auto-printing no longer differs for functions with
a user defined print.function, thanks to Bill Dunlap's report.
* On Windows, writeClipboard(.., format = <n>) now does correctly
pass format to the underlying C code, thanks to a bug report
(with patch) by Jenny Bryan.
* as.data.frame() treats 1D arrays the same as vectors, PR#17570.
* Improvements in smoothEnds(x, *) working with NAs (towards
runmed() working in that case, in the next version of R).
* vcov(glm(<quasi>), dispersion = *) works correctly again, fixing
PR#17571 thanks to Pavel Krivitsky.
* R CMD INSTALL of binary packages on Windows now works also with
per-directory locking.
* R CMD INSTALL and install.packages() on Windows are now more
robust against a locked file in an earlier installation of the
package to be installed. The default value of option
install.lock on Windows has been changed to TRUE.
* On Unix alikes (when readline is active), only expand tilde (~)
file names starting with a tilde, instead of almost all tildes.
* In R documentation (*.Rd) files, \item [..] is no longer treated
specially when rendered in LaTeX and hence pdf, but rather shows
the brackets in all cases.
* Fri Apr 26 2019 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 3.6.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* Serialization format version 3 becomes the default for
serialization and saving of the workspace (save(), serialize(),
saveRDS(), compiler::cmpfile()). Serialized data in format 3
cannot be read by versions of R prior to version 3.5.0.
Serialization format version 2 is still supported and can be
selected by version = 2 in the save/serialization functions. The
default can be changed back for the whole R session by setting
environment variables R_DEFAULT_SAVE_VERSION and
R_DEFAULT_SERIALIZE_VERSION to 2. For maximal
back-compatibility, files vignette.rds and partial.rdb generated
by R CMD build are in serialization format version 2, and resave
by default produces files in serialization format version 2
(unless the original is already in format version 3).
* The default method for generating from a discrete uniform
distribution (used in sample(), for instance) has been changed.
This addresses the fact, pointed out by Ottoboni and Stark, that
the previous method made sample() noticeably non-uniform on large
populations. See PR#17494 for a discussion. The previous method
can be requested using RNGkind() or RNGversion() if necessary for
reproduction of old results. Thanks to Duncan Murdoch for
contributing the patch and Gabe Becker for further assistance.
The output of RNGkind() has been changed to also return the
'kind' used by sample().
NEW FEATURES:
* Sys.setFileTime() has been vectorized so arguments path and time
of length greater than one are now supported.
* axis() gets new option gap.axis = NA for specifying a
multiplication factor for the minimal "gap" (distance) between
axis labels drawn. Its default is 1 for labels _parallel_ to the
axis, and 0.25 for perpendicular ones.
Perpendicular labels no longer overlap, fixing bug PR#17384.
* The default method of plot() gains new arguments xgap.axis = NA
and ygap.axis = NA to be passed to the x- and y- axis(..,
gap.axis=*) calls.
* removeSource() now works not only for functions but also for some
language objects.
* as.call(), rep.int(), rep_len() and nchar() dispatch internally.
* is(object, class2) looks for class2 in the calling namespace
after looking in the namespace of class(object).
* extendrange(.., f) with a length-2 f now extends separately to
the left and the right.
* lengths() dispatches internally to S4 methods.
* download.file() on Windows now uses URLdecode() to determine the
file extension, and uses binary transfer (mode = "wb") also for
file extension .rds.
The help page for download.file() now contains the same
information on all platforms.
* Setting C locale for collation _via_ environment variables LC_ALL
and LC_COLLATE and _via_ a call to Sys.setlocale() now takes
precedence over environment variable R_ICU_LOCALE.
* There is a new function, nullfile(), to give the file name of the
null system device (e.g., /dev/null) on the current platform.
* There are two new options, keep.parse.data and
keep.parse.data.pkgs, which control whether parse data are
included into sources when keep.source or keep.source.pkgs is
TRUE. By default, keep.parse.data.pkgs is now FALSE, which
changes previous behavior and significantly reduces space and
time overhead when sources are kept when installing packages.
* In rapply(x, ..), x can also be "list-like" and of length >=
2^{31}.
* trimws() gets new optional whitespace argument, allowing more
extensive definitions of "space", such as including Unicode
spaces (as wished in PR#17431).
* weighted.mean() no longer coerces the weights to a double/numeric
vector, since sum() now handles integer overflow. This makes
weighted.mean() more polymorphic and endomorphic, but be aware
that the results are no longer guaranteed to be a vector of type
double.
* When loading namespaces, S3 method registrations which overwrite
previous registrations are now noted by default (using
packageStartupMessage()).
* compiler::cmpfile() gains a version argument, for use when the
output file should be saved in serialization format 2.
* The axis labeling in the default method of pairs() may now be
toggled by new options horOdd and verOdd.
* (Not Windows nor macOS.) Package tcltk now supports an
environment variable R_DONT_USE_TK which if set disables Tk
initialization. This is intended for use to circumvent errors in
loading the package, e.g. with recent Linux running under an
address sanitizer.
* The numeric method of all.equal() gets optional arguments countEQ
and formatFUN. If countEQ is true, the mean error is more
sensible when many entries are *eq*ual.
* outer(x,y, FUN = "*") is more efficient using tcrossprod(u,v)
instead of u %*% t(v).
* vcov(<mlm>) is more efficient via new optional arguments in
summary.mlm().
* The default method of summary() gets an option to choose the
_kind_ of quantile()s to use; wish of PR#17438.
* Fitting multiple linear models _via_ lm() does work with _matrix_
offsets, as suggested in PR#17407.
* The new functions mem.maxVSize() and mem.maxMSize() allow the
maximal size of the vector heap and the maximal number of nodes
allowed in the current R process to be queried and set.
* news() gains support for NEWS.md files.
* An effort has been started to have our reference manuals, i.e.,
all help pages. show platform-independent information (rather
than Windows or Unix-alike specifics visible only on that
platform). Consequently, the Windows version of X11() / x11()
got identical formal arguments to the Unix one.
* sessionInfo()$running has been factored out in a new variable
osVersion.
* slice.index() now also works for multi-dimensional margins.
* untar() used with an external tar command assumes this supports
decompression including xz and automagically detecting the
compression type. This has been true of all mainstream
implementations since 2009 (for GNU tar, since version 1.22):
older implementations are still supported _via_ the new argument
support_old_tars whose default is controlled by environment
variable R_SUPPORT_OLD_TARS. (It looks like NetBSD and OpenBSD
have 'older' tar commands for this purpose.)
* The new function asplit() allow splitting an array or matrix by
its margins.
* New functions errorCondition() and warningCondition() provide a
convenient way to create structured error and warning objects.
.Deprecated() now signals a warning of class "deprecatedWarning",
and .Defunct() now signals an error of class "defunctError".
* Many 'package not found' errors are now signaled as errors of
class "packageNotFoundError".
* As an experimental feature, when loadNamespace() fails because
the requested package is not available the error is initially
signaled with a retry_loadNamespace restart available. This
allows a calling handler to try to install the package and
continue.
* S3method() directives in NAMESPACE can now also be used to
perform _delayed_ S3 method registration.
* Experimentally, setting environment variable
_R_CHECK_LENGTH_1_LOGIC2_ will lead to warnings (or errors if the
variable is set to a 'true' value) when && or || encounter and
use arguments of length more than one.
* Added "lines" and "chars" coordinate systems to grconvertX() and
grconvertY().
* getOption() is more efficient notably for the rare case when
called with two arguments, from several contributors in PR#17394.
* In .col(dim) and .row(dim), dim now may also be an integer-valued
"double".
* sQuote() and dQuote() get an explicit q argument with obvious
default instead of using getOption("fancyQuotes") implicitly and
unconditionally.
* unzip() can list archives with comments and with spaces in file
names even using an external unzip command.
* Command line completion has a new setting rc.settings(dots =
FALSE) to remove ... from the list of possible function
arguments.
* library() no longer checks packages with compiled code match
R.version$platform. loadNamespace() never has, and increasingly
the 'canonical name' does not reflect the important
characteristics of compiled code.
* The primitive functions drop() and unclass() now avoid
duplicating their data for atomic vectors that are large enough,
by returning ALTREP wrapper objects with adjusted attributes.
R-level assignments to change attributes will also use wrapper
objects to avoid duplicating data for larger atomic vectors. R
functions like structure() and unname() will therefore not
duplicate data in these settings. Generic vectors as produced by
list() are not yet covered by this optimization but may be in due
course.
* In formals(), envir becomes an optional argument instead of being
hardwired.
* Instead of signalling an error for an invalid S4 object x, str(x)
now gives a warning and subsequently still shows most parts of x,
e.g., when slots are missing.
* gamma(x) and lgamma(x) no longer warn when correctly returning
Inf or underflowing to zero. This helps maximum likelihood and
similar computations.
* convertColor() is now vectorized, so a lot faster for converting
many colours at once. The new argument vectorized to
colorConverter() ensures that non-vectorized colour converters
still work. (Thanks to Brodie Gaslam.)
* download.file() and url() get new argument headers for custom
HTTP headers, e.g., allowing to perform basic http
authentication, thanks to a patch contributed by G'abor Cs'ardi.
* File-based connection functions file(), gzfile(), bzfile() and
xzfile() now signal an error when used on a directory.
* For approx(), splinefun() _etc_, a new setting ties =
c("ordered", <fun>) allows skipping the sorting and still treat
ties.
* format(x) gives a more user friendly error message in the case
where no method is defined. A minimal method is provided in
format.default(x) when isS4(x) is true.
* which(x) now also works when x is a long vector, thanks to
Suharto Anggono's PR#17201. *NB*: this may return a double
result, breaking the previous guarantee of an integer result.
* seq.default() is more careful to return an integer (as opposed to
double) result when its arguments are large and/or classed
objects; see comment #9 of Suharto Anggono's PR#17497.
* The plot() method for lm and glm fits, plot.lm(), gains a new
option iter.smooth with a default of 0 for binomial fits, no
longer down-weighting when smoothing the residuals.
* zip() passes its list of files _via_ standard input to the
external command when too long for the command line (on some
platforms).
* data() gains an overwrite argument.
* t.test() now also returns the standard error (in list component
stderr).
* model.matrix(*, contrasts.arg = CC) now warns about invalid
contrasts.args.
* Performance of substr() and substring() has been improved.
* stopifnot() has been simplified thanks to Suharto Anggono's
proposals to become considerably faster for cheap expressions.
* The default 'user agent' has been changed when accessing http://
and https:// sites using libcurl. (A site was found which caused
libcurl to infinite-loop with the previous default.)
* sessionInfo() now also contains RNGkind() and prints it when it
differs from the default; based on a proposal and patch by Gabe
Becker in PR#17535. Also, RNGversion(getRversion()) works
directly.
* library() and require() now allow more control over handling
search path conflicts when packages are attached. The policy is
controlled by the new conflicts.policy option.
* barplot() gets a formula method, thanks to a patch proposal by
Arni Magnusson in PR#17521.
* pmax() and pmin(x) now also work for long vectors, thanks to
Suharto Anggono's PR#17533.
* bxp() now warns when omitting duplicated arguments.
* New hcl.colors() function to provide wide range of HCL-based
colour palettes with much better perceptual properties than the
existing RGB/HSV-based palettes like rainbow().
Also a new hcl.pals() function to list available palette names
for hcl.colors().
Contributed by Achim Zeileis.
* The default colours for image() and filled.contour() are now
based on hcl.colors().
* The palette-generating functions rainbow(), gray.colors(), etc.
get a new rev argument to facilitate reversing the order of
colors.
* New str2lang() and str2expression() as streamlined versions of
parse(text=., keep.source=FALSE) allow to abstract typical call
constructions, e.g., in formula manipulations. (Somewhat
experimental)
* Add update_PACKAGES() for incrementally updating a package
repository index, instead of rebuilding the index from scratch.
Thanks to Gabe Becker in PR#17544 for the patch, based on part of
his switchr package.
INSTALLATION on a UNIX-ALIKE:
* The options selected for the C++ compiler default to the C++11
standard if supported, otherwise to the C++98 standard.
* Visibility macros such as C_VISIBILITY can now be user-set
(including to empty), e.g. in config.site.
* Macro FCLIBS, which has sometimes been needed on Solaris, has
been renamed to FCLIBS_XTRA.
* Macro F77 is always set to the value of FC, so the latter should
be set to user-select the Fortran compiler for both fixed-form
and free-form Fortran. In particular, gfortran is now the first
choice for F77, not f95.
Macros FFLAGS and FCFLAGS remain distinct to allow for a compiler
which needs a flag to select free- or fixed-form Fortran (most
use the source-file extension to choose: .f is fixed-form and
.f90 and .f95 are free-form).
If only one of them is set, its value is used for both.
* The special-casing of CFLAGS, CXXFLAGS and FFLAGS for Intel
compilers on Linux has been removed: we do not have recent
experience but the generic defaults now chosen are the same as
those previously special-cased for x86_64.
If necessary, override the defaults on the configure command line
or in file config.site.
* Long-untested configure support for HP-UX and very old versions
of Linux has been removed.
* configure --with-blas (without specifying a value) includes
OpenBLAS in its search (before ATLAS and a generic BLAS). This
follows recent versions of the ax_blas autoconf macro.
* The configure macro MAKEINFO has been updated to TEXI2ANY.
* Support for make install-strip has been enhanced.
PACKAGE INSTALLATION:
* Source package installation is by default 'staged': the package
is installed into a temporary location under the final library
directory and moved into place once the installation is complete.
The benefit is that partially-installed packages are hidden from
other R sessions.
The overall default is set by environment variable
R_INSTALL_STAGED. R CMD INSTALL has new options --staged-install
and --no-staged-install, and packages can use the StagedInstall
field in their DESCRIPTION file to opt out. (That opt-out is a
temporary measure which may be withdrawn in future.)
Staged installation requires either --pkglock or --lock, one of
which is used by default.
* The interpretation of source code with extension .f is changing.
Previously this denoted FORTRAN 77 code, but current compilers no
longer have a FORTRAN 77 mode and interpret it as 'fixed-form'
Fortran 90 (or later where supported) code. Extensions .f90 and
.f95 continue to indicate 'free-form' Fortran code.
Legal FORTRAN 77 code is also legal fixed-form Fortran 9x;
however this change legitimizes the use of later features, in
particular to replace features marked 'obsolescent' in Fortran 90
and 'deleted' in Fortran 2018 which gfortran 8.x and later warn
about.
* Packages containing files in the src directory with extensions
.f90 or .f95 are now linked using the C or C++ compiler rather
than the Fortran 9x compiler. This is consistent with fixed-form
Fortran code and allows mixing of C++ and free-form Fortran on
most platforms.
Consequentially, a package which includes free-form Fortran 9x
code which uses OpenMP should include SHLIB_OPENMP_CFLAGS (or the
CXXFLAGS version if they also include C++ code) in PKG_LIBS
rather than SHLIB_OPENMP_FCFLAGS - fortunately on almost all
current platforms they are the same flag.
* Macro PKG_FFLAGS will be used for the compilation of both
fixed-form and free-form Fortran code unless PKG_FCFLAGS is also
set (in src/Makevars or src/Makevars.win).
* The make macro F_VISIBILITY is now preferred for both fixed-form
and free-form Fortran, for use in src/Makevars and similar.
* R CMD INSTALL gains a new option --strip which (where supported)
strips installed shared object(s): this can also be achieved by
setting the environment variable _R_SHLIB_STRIP_ to a true value.
The new option --strip-lib attempts stripping of static and
shared libraries installed under lib.
These are most useful on platforms using GNU binutils (such as
Linux) and compiling with -g flags.
* There is more support for installing UTF-8-encoded packages in a
strict Latin-1 locale (and probably for other Latin locales):
non-ASCII comments in R code (and NAMESPACE files) are worked
around better.
UTILITIES:
* R CMD check now optionally checks makefiles for correct and
portable use of the SHLIB_OPENMP_*FLAGS macros.
* R CMD check now evaluates \Sexpr{} expressions (including those
in macros) before checking the contents of Rd files and so
detects issues both in evaluating the expressions and in the
expanded contents.
* R CMD check now lists missing packages separated by commas and
with regular quotes such as to be useful as argument in calling
install.packages(c(..)); from a suggestion by Marcel Ramos.
* tools::Rd2latex() now uses UTF-8 as its default output encoding.
* R CMD check now checks line endings of files with extension .hpp
and those under inst/include. The check now includes that a
non-empty file is terminated with a newline.
R CMD build will correct line endings in such files.
* R CMD check now tries re-building all vignettes rather than
stopping at the first error: whilst doing so it adds 'bookmarks'
to the log. By default (see the 'R Internals' manual) it
re-builds each vignette in a separate process.
It now checks for duplicated vignette titles (also known as
'index entries'): they are used as hyperlinks on CRAN package
pages and so do need to be unique.
* R CMD check has more comprehensive checks on the data directory
and the functioning of data() in a package.
* R CMD check now checks autoconf-generated configure files have
their corresponding source files, including optionally attempting
to regenerate them on platforms with autoreconf.
* R CMD build has a new option --compression to select the
compression used for the tarball.
* R CMD build now removes src/*.mod files on all platforms.
C-LEVEL FACILITIES:
* New pointer protection C functions R_PreserveInMSet and
R_ReleaseFromMSet have been introduced to replace UNPROTECT_PTR,
which is not safe to mix with UNPROTECT (and with
PROTECT_WITH_INDEX). Intended for use in parsers only.
* NAMEDMAX has been raised to 7 to allow further protection of
intermediate results from (usually ill-advised) assignments in
arguments to BUILTIN functions. Properly written package code
should not be affected.
* R_unif_index is now considered to be part of the C API.
* R_GetCurrentEnv() allows C code to retrieve the current
environment.
DEPRECATED AND DEFUNCT:
* Argument compressed of untar() is deprecated - it is only used
for external tar commands which increasingly for extraction
auto-detect compression and ignore their zjJ flags.
* var(f) and hence sd(f) now give an error for factor arguments;
they gave a deprecation warning since R 3.2.3, PR#16564.
* Package tools' vignetteDepends() has been deprecated (it called a
function deprecated since Feb 2016), being partly replaced by
newly exported vignetteInfo().
* The f77_f2c script has been removed: it no longer sufficed to
compile the .f files in R.
* The deprecated legacy support of make macros such as CXX1X has
been removed: use the CXX11 forms instead.
* Make macro F77_VISIBILITY is deprecated in favour of
F_VISIBILITY.
* Make macros F77, FCPIFCPLAGS and SHLIB_OPENMP_FCFLAGS are
deprecated in favour of FC, FPICFLAGS and SHLIB_OPENMP_FFLAGS
respectively.
* $.data.frame had become an expensive version of the default
method, so has been removed. (Thanks to Radford Neal for picking
this up and to Duncan Murdoch for providing a patch.)
BUG FIXES:
* replayPlot(r) now also works in the same R session when r has
been "reproduced" from serialization, typically after saving to
and reading from an RDS file.
* substr() and substring() now signal an error when the input is
invalid UTF-8.
* file.copy() now works also when its argument to is of length
greater than one.
* mantelhaen.test() no longer suffers from integer overflow in
largish cases, thanks to Ben Bolker's PR#17383.
* Calling setGeneric("foo") in a package no longer fails when the
enclosing environment of the implicit generic foo() is
.GlobalEnv.
* untar(file("<some>.tar.gz"), *) now gives a better error message,
suggesting to use gzfile() instead.
* Method dispatch uses more relevant environments when looking up
class definitions.
* The documentation for identify() incorrectly claimed that the
indices of identified points were returned in the order that the
points were selected. identify() now has a new argument order to
allow the return value to include the order in which points were
identified; the documentation has been updated. Reported by
Richard Rowe and Samuel Granjeaud.
* order(...., decreasing=c(TRUE, FALSE)) could fail in some cases.
Reported from StackOverflow via Karl Nordstr"om.
* User macros in Rd files now accept empty and multi-line
arguments.
* Changes in print.*(), thanks to Lionel Henry's patches in
PR#17398:
* Printing lists, pairlists or attributes containing calls with
S3 class no longer evaluate those.
* Printing S4 objects within lists and pairlists dispatches
with show() rather than print(), as with auto-printing.
* The indexing tags (names or [[<n>]]) of recursive data
structures are now printed correctly in complex cases.
* Arguments supplied to print() are now properly forwarded to
methods when printing lists, pairlists or attributes
containing S3 objects.
* The print parameters are now preserved when printing S3
objects or deparsing symbols and calls. Previously, printing
lists containing S3 objects or expressions would reset these
parameters.
* Printing lists, pairlists or attributes containing functions
now uses srcref attributes if present.
* Calling install.packages() with a length zero pkgs argument now
is a no-op (PR#17422).
* unlist(x) now returns a correct factor when x is a nested list
with factor leaves, fixing PR#12572 and PR#17419.
* The documentation help(family) gives more details about the aic
component, thanks to Ben Bolker's prompting.
* The documentation for attributes and `attributes<-` now gives x
as name of the first and main argument which the implementation
has been requiring, fixing PR#17434. For consistency, the first
argument name is also changed from obj to x for
`mostattributes<-`.
* strwidth() now uses par("font") as default font face (PR#17352).
* plot(<table>, log="x") no longer warns about log.
* The print() method for "htest" objects now formats the test
statistic and parameter directly and hence no longer rounds to
units _before_ the decimal point. Consequently, printing of
t.test() results with a small number of digits now shows
non-large df's to the full precision (PR#17444).
* kruskal.test() and fligner.test() no longer erroneously insist on
numeric g group arguments (PR#16719).
* Printing a news db via the browser now does a much better job
(PR#17433).
* print.aov() missed column names in the multivariate case due to
misspelling (reported by Chris Andrews).
* axis() now creates valid at locations also for small subnormal
number ranges in log scale plots.
* format.POSIXlt() now also recycles the zone and gmtoff list
components to full length when needed, and its internal C code
detects have_zone in more cases. In some cases, this changes its
output to become compatible with format.POSIXct().
* On Windows, detectCores() in package parallel now detects
processors in all processor groups, not just the group R is
running in (impacts particularly systems with more than 64
logical processors). Reported by Arunkumar Srinivasan.
* On Windows, socketSelect() would hang with more than 64 sockets,
and hence parallel::clusterApplyLB() would hang with more than 64
workers. Reported by Arunkumar Srinivasan.
* as(1L, "double") now does coerce (PR#17457).
* lm.influence(), influence.measures(), rstudent() etc now work
(more) correctly for multivariate models ("mlm"), thanks to
(anonymous) stackoverflow remarks.
* sample.int(2.9, *, replace=TRUE) again behaves as documented and
as in R < 3.0.0, namely identically to sample.int(2, ..).
* Fixes to convertColor() for chromatic adaptation; thanks to
Brodie Gaslam PR#17473.
* Using \Sexpr[stage=install]{..} to create an Rd section no longer
gives a warning in R CMD check; problem originally posted by
G'abor Cs'ardi, then reported as PR#17479 with a partial patch by
Duncan Murdoch.
* Parse data now include a special node for equal assignment.
* split.default() no longer relies on [[<-(), so it behaves as
expected when splitting an object by a factor with the empty
string as one of its levels. Thanks to Brad Friedman for the
report.
* Line numbers in messages about .Rd files are now more reliable,
thanks to a patch from Duncan Murdoch.
* In the numeric method for all.equal(), a numeric scale argument
is now checked to be positive and allowed to be of length > 1.
(The latter worked originally and with a warning in recent
years).
* Deferred string conversions now record the OutDec option setting
when not equal to the default. Reported by Michael Sannella.
* When y is numeric and f a factor, plot(y ~ f) nicely uses "y" and
"f" as y- and x-labels. The more direct boxplot(y ~ f) now does
too. The new argument ann = FALSE may be used to suppress these.
* Subassignment to no/empty rows of a data frame is more consistent
and typically a no-op in all cases instead of sometimes an error;
part of Emil Bode's PR#17483.
* Calls like formatC(*, zero.print = "< 0.001") no longer give an
error and are further improved via new optional argument
replace.zero. Reported by David Hugh-Jones.
* methods::formalArgs("<fn>") now finds the same function as
formals("<fn>"), fixing Emil Bode's PR#17499.
* The methods package better handles duplicated class names across
packages.
* The default method of seq() now avoids integer overflow, thanks
to the report and "cumsum" patch of Suharto Anggono's PR#17497.
* sub() no longer loses encodings for non-ASCII replacements
(PR#17509).
* Fix for rotated raster image on X11 device. (Partial fix for
PR#17148; thanks to Mikko Korpela).
* formula(model.frame(frml, ..)) now returns frml in all cases,
thanks to Bill Dunlap. The previous behavior is available as
DF2formula(<model.frame>).
* ar.ols() also returns scalar var.pred in univariate case
(PR#17517).
* normalizePath() now treats NA path as non-existent and normalizes
it to NA. file.access() treats NA file name as non-existent.
file.edit() and connection functions such as file() now treat NA
file names as errors.
* The internal regularize.values() auxiliary of approx(),
splinefun() etc now warns again when there are ties and the
caller did not specify ties. Further, it no longer duplicates x
and y unnecessarily when x is already sorted (PR#17515).
* strtoi("", base) now gives NA on all platforms, following its
documentation. Reported by Michael Chirico.
* In the definition of an S4 class, prototype elements are checked
against the slots of the class, with giving a prototype for an
undefined slot now being an error. (Reported by Bill Dunlap.)
* From setClassUnion(), if environment variable
_R_METHODS_SHOW_CHECKSUBCLASSES is set to true, the internal
.checkSubclasses() utility prints debugging info to see where it
is used.
* max.col(m) with an m of zero columns now returns integer NA
(instead of 1).
* axTicks() no longer returns small "almost zero" numbers (in
exponential format) instead of zero, fixing Ilario Gelmetti's
PR#17534.
* isSymmetric(matrix(0, dimnames=list("A","b"))) is FALSE again, as
always documented.
* The cairo_pdf graphics device (and other Cairo-based devices) now
clip correctly to the right and bottom border.
There was an off-by-one-pixel bug, reported by Lee Kelvin.
* as.roman(3) <= 2:4 and all other comparisons now work, as do
group "Summary" function calls such as max(as.roman(sample(20)))
and as.roman(NA). (Partly reported by Bill Dunlap in PR#17542.)
* reformulate("x", response = "sin(y)") no longer produces extra
back quotes, PR#17359, and gains new optional argument env.
* When reading console input from stdin with re-encoding (R
- -encoding=enc < input) the code on a Unix-alike now ensures that
each converted input line is terminated with a newline even if
re-encoding fails.
* as.matrix.data.frame() now produces better strings from logicals,
thanks to PR#17548 from Gabe Becker.
* The S4 generic signature of rowSums(), rowMeans(), colSums() and
colMeans() is restricted to "x".
* match(x, tab) now works for long _character_ vectors x, thanks to
PR#17552 by Andreas Kersting.
* Class unions are unloaded when their namespace is unloaded
(PR#17531, adapted from a patch by Brodie Gaslam).
* selectMethod() is robust to ANY-truncation of method signatures
(thanks to Herve Pages for the report).
* Mon Mar 11 2019 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 3.5.3:
INSTALLATION on a UNIX-ALIKE:
* Detection of flags for C++98/11/14/17 has been improved: in
particular if CXX??STD is set, it is tried first with no
additional flags.
PACKAGE INSTALLATION:
* New macro F_VISIBILITY as an alternative to F77_VISIBILITY. This
will become the preferred form in R 3.6.0.
BUG FIXES:
* writeLines(readLines(fnam), fnam) now works as expected, thanks
to Peter Meissner's PR#17528.
* setClassUnion() no longer warns, but uses message() for now, when
encountering "non local" subclasses of class members.
* stopifnot(exprs = T) no longer fails.
* Tue Jan 15 2019 Todd R <toddrme2178@gmail.com>
- Add architecture-independent package directory.
Taken from the Fedora version of R.
- Add RPM macros to ease installation of R packages.
- Fix building on older versions of openSUSE.
* Wed Dec 19 2018 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 3.5.2:
PACKAGE INSTALLATION:
* New macro CXX_VISIBILITY analogous to C_VISIBILITY (which several
packages have been misusing for C++ code) for the default C++
compiler (but not necessarily one used for non-default C++
dialects like C++14).
TESTING:
* The random number generator tests in tests/p-r-random-tests.R no
longer fail occasionally as they now randomly sample from
"certified" random seeds.
BUG FIXES:
* The "glm" method of drop1() miscalculated the score test
(test="Rao") when the model contained an offset.
* Linear multiple empty models such as lm(y ~ 0) now have a
correctly dimensioned empty coefficient matrix; reported by Brett
Presnell.
* vcov(<empty mlm>) and hence confint() now work (via a consistency
change in summary.lm()).
* confint(<multiple lm()>) now works correctly; reported on R-devel
by Steven Pav.
* quade.test() now also works correctly when its arguments are not
yet sorted along groups, fixing PR#15842.
* Installation on a Unix-alike tries harder to link to the pthread
library where required (rather than relying on OpenMP to provide
it: configuring with --disable-openmp was failing on some Linux
systems).
* The data.frame method for print(x) is fast now also for large
data frames x and got an optional argument max, thanks to
suggestions by Juan Telleria.
* hist() no longer integer overflows in very rare cases, fixing
PR#17450.
* untar() ignored a character compressed argument: however many
external tar programs ignore the flags which should have been set
and automagically choose the compression type, and if appropriate
gzip or bzip2 compression would have been chosen from the magic
header of the tarball.
* zapsmall(x) now works for more "number-like" objects.
* The tools-internal function called from R CMD INSTALL now gets a
warnOption = 1 argument and only sets options(warn = warnOption)
when that increases the warning level (PR#17453).
* Analogously, the tools-internal function called from R CMD check
gets a warnOption = 1 argument and uses the larger of that and
getOption("warn"), also allowing to be run with increased warning
level.
* Parse data now have deterministic parent nodes (PR#16041).
* Calling match() with length one x and POSIXlt table gave a
segfault (PR#17459).
* Fork clusters could hang due to a race condition in cluster
initialization (makeCluster()).
* nextn(n) now also works for larger n and no longer loops
infinitely for e.g, n <- 214e7.
* cooks.distance() and rstandard() now work correctly for multiple
linear models ("mlm").
* polym() and corresponding lm() prediction now also work for a
boundary "vector" case fixing PR#17474, reported by Alexandre
Courtiol.
* With a very large number of variables terms() could segfault
(PR#17480).
* cut(rep(0, 7)) now works, thanks to Joey Reid and Benjamin Tyner
(PR#16802).
* download.file(*, method = "curl", cacheOK = FALSE) should work
now on Windows, thanks to Kevin Ushey's patch in PR#17323.
* duplicated(<dataframe with 'f'>) now works, too, thanks to
Andreas Kersting's PR#17485; ditto for anyDuplicated().
* legend(*, cex = 1:2) now works less badly.
* The print() method for POSIXct and POSIXlt now correctly obeys
getOption("max.print"), fixing a long-standing typo, and it also
gets a corresponding optional max argument.
* Unserialization of raw vectors serialized in ASCII representation
now works correctly.
* <data frame>[TRUE, <new>] <- list(c1, c2) now works correctly,
thanks to Suharto Anggono's PR#15362 and Emil Bode's patch in
PR#17504.
* seq.int(*, by=by, length=n) no longer wrongly "drops fractional
parts" when by is integer, thanks to Suharto Anggono's report
PR#17506.
* Buffering is disabled for file() connections to non-regular files
(like sockets), as well as fifo() and pipe() connections. Fixes
PR#17470, reported by Chris Culnane.
* Mon Jul 02 2018 detlef.steuer@gmx.de
- CHANGES IN R 3.5.1 :
BUG FIXES:
* file("stdin") is no longer considered seekable.
* dput() and dump() are no longer truncating when
options(deparse.max.lines = *) is set.
* Calls with an S3 class are no longer evaluated when printed,
fixing part of PR#17398, thanks to a patch from Lionel Henry.
* Allow file argument of Rscript to include space even when it is
first on the command line.
* callNextMethod() uses the generic from the environment of the
calling method. Reported by Herv'e Pag`es with well documented
examples.
* Compressed file connections are marked as blocking.
* optim(*, lower = c(-Inf, -Inf)) no longer warns (and switches the
method), thanks to a suggestion by John Nash.
* predict(fm, newdata) is now correct also for models where the
formula has terms such as splines::ns(..) or stats::poly(..),
fixing PR#17414, based on a patch from Duncan Murdoch.
* simulate.lm(glm(*, gaussian(link = <non-default>))) has been
corrected, fixing PR#17415 thanks to Alex Courtiol.
* unlist(x) no longer fails in some cases of nested empty lists.
Reported by Steven Nydick.
* qr.coef(qr(<all 0, w/ colnames>)) now works. Reported by Kun
Ren.
* The radix sort is robust to vectors with >1 billion elements (but
long vectors are still unsupported). Thanks to Matt Dowle for the
fix.
* Terminal connections (e.g., stdin) are no longer buffered. Fixes
PR#17432.
* deparse(x), dput(x) and dump() now respect c()'s argument names
recursive and use.names, e.g., for x <- setNames(0, "recursive"),
thanks to Suharto Anggono's PR#17427.
* Unbuffered connections now work with encoding conversion.
Reported by Stephen Berman.
* .Renviron on Windows with Rgui is again by default searched for
in user documents directory when invoked _via_ the launcher icon.
Reported by Jeroen Ooms.
* printCoefmat() now also works with explicit right=TRUE.
* print.noquote() now also works with explicit quote=FALSE.
* The default method for pairs(.., horInd=*, verInd=*) now gets the
correct order, thanks to reports by Chris Andrews and Gerrit
Eichner. Additionally, when horInd or verInd contain only a
subset of variables, all the axes are labeled correctly now.
* agrep("..|..", .., fixed=FALSE) now matches when it should,
thanks to a reminder by Andreas Kolter.
* str(ch) now works for more invalid multibyte strings.
* 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.
* Tue May 03 2016 detlef.steuer@gmx.de
- tre.patch was removed.
* Tue May 03 2016 detlef.steuer@gmx.de
- and libbz2-devel needed, too.
* Tue May 03 2016 detlef.steuer@gmx.de
- added BuildRequires: bzip2
for i586.
* Tue May 03 2016 detlef.steuer@gmx.de
- upstream release 3.3.0
CHANGES IN R 3.3.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* nchar(x, *)'s argument keepNA governing how the result for NAs in
x is determined, gets a new default keepNA = NA which returns NA
where x is NA, except for type = "width" which still returns 2,
the formatting / printing width of NA.
* All builds have support for https: URLs in the default methods
for download.file(), url() and code making use of them.
Unfortunately that cannot guarantee that any particular https:
URL can be accessed. For example, server and client have to
successfully negotiate a cryptographic protocol (TLS/SSL, ...)
and the server's identity has to be verifiable _via_ the
available certificates. Different access methods may allow
different protocols or use private certificate bundles: we
encountered a https: CRAN mirror which could be accessed by one
browser but not by another nor by download.file() on the same
Linux machine.
NEW FEATURES:
* The print method for methods() gains a byclass argument.
* New functions validEnc() and validUTF8() to give access to the
validity checks for inputs used by grep() and friends.
* Experimental new functionality for S3 method checking, notably
isS3method().
Also, the names of the R 'language elements' are exported as
character vector tools::langElts.
* str(x) now displays "Time-Series" also for matrix (multivariate)
time-series, i.e. when is.ts(x) is true.
* (Windows only) The GUI menu item to install local packages now
accepts *.tar.gz files as well as *.zip files (but defaults to
the latter).
* New programmeR's utility function chkDots().
* D() now signals an error when given invalid input, rather than
silently returning NA. (Request of John Nash.)
* formula objects are slightly more "first class": e.g., formula()
or new("formula", y ~ x) are now valid. Similarly, for "table",
"ordered" and "summary.table". Packages defining S4 classes with
the above S3/S4 classes as slots should be reinstalled.
* New function strrep() for repeating the elements of a character
vector.
* rapply() preserves attributes on the list when how = "replace".
* New S3 generic function sigma() with methods for extracting the
estimated standard deviation aka "residual standard deviation"
from a fitted model.
* news() now displays R and package news files within the HTML help
system if it is available. If no news file is found, a visible
NULL is returned to the console.
* as.raster(x) now also accepts raw arrays x assuming values in
0:255.
* Subscripting of matrix/array objects of type "expression" is now
supported.
* type.convert("i") now returns a factor instead of a complex value
with zero real part and missing imaginary part.
* Graphics devices cairo_pdf() and cairo_ps() now allow non-default
values of the cairographics 'fallback resolution' to be set.
This now defaults to 300 on all platforms: that is the default
documented by cairographics, but apparently was not used by all
system installations.
* file() gains an explicit method argument rather than implicitly
using getOption("url.method", "default").
* Thanks to a patch from Tomas Kalibera, x[x != 0] is now typically
faster than x[which(x != 0)] (in the case where x has no NAs, the
two are equivalent).
* read.table() now always uses the names for a named colClasses
argument (previously names were only used when colClasses was too
short). (In part, wish of PR#16478.)
* (Windows only) download.file() with default method = "auto" and a
ftps:// URL chooses "libcurl" if that is available.
* The out-of-the box Bioconductor mirror has been changed to one
using https://: use chooseBioCmirror() to choose a http:// mirror
if required.
* The data frame and formula methods for aggregate() gain a drop
argument.
* available.packages() gains a repos argument.
* The undocumented switching of methods for url() on https: and
ftps: URLs is confined to method = "default" (and documented).
* smoothScatter() gains a ret.selection argument.
* qr() no longer has a ... argument to pass additional arguments to
methods.
* [ has a method for class "table".
* It is now possible (again) to replayPlot() a display list
snapshot that was created by recordPlot() in a different R
session.
It is still not a good idea to use snapshots as a persistent
storage format for R plots, but it is now not completely silly to
use a snapshot as a format for transferring an R plot between two
R sessions.
The underlying changes mean that packages providing graphics
devices (e.g., Cairo, RSvgDevice, cairoDevice, tikzDevice) will
need to be reinstalled.
Code for restoring snapshots was contributed by Jeroen Ooms and
JJ Allaire.
Some testing code is available at <URL:
https://github.com/pmur002/R-display-list>.
* tools::undoc(dir = D) and codoc(dir = D) now also work when D is
a directory whose normalizePath()ed version does not end in the
package name, e.g. from a symlink.
* abbreviate() has more support for multi-byte character sets - it
no longer removes bytes within characters and knows about Latin
vowels with accents. It is still only really suitable for (most)
European languages, and still warns on non-ASCII input.
abbreviate(use.classes = FALSE) is now implemented, and that is
more suitable for non-European languages.
* match(x, table) is faster (sometimes by an order of magnitude)
when x is of length one and incomparables is unchanged, thanks to
Peter Haverty (PR#16491).
* More consistent, partly not back-compatible behavior of NA and
NaN coercion to complex numbers, operations less often resulting
in complex NA (NA_complex_).
* lengths() considers methods for length and [[ on x, so it should
work automatically on any objects for which appropriate methods
on those generics are defined.
* The logic for selecting the default screen device on OS X has
been simplified: it is now quartz() if that is available even if
environment variable DISPLAY has been set by the user.
The choice can easily be overridden _via_ environment variable
R_INTERACTIVE_DEVICE.
* On Unix-like platforms which support the getline C library
function, system(*,intern = TRUE) no longer truncates (output)
lines longer than 8192 characters, thanks to Karl Millar.
(PR#16544)
* rank() gains a ties.method = "last" option, for convenience (and
symmetry).
* regmatches(invert = NA) can now be used to extract both
non-matched and matched substrings.
* data.frame() gains argument fix.empty.names; as.data.frame.list()
gets new cut.names, col.names and fix.empty.names.
* plot(x ~ x, *) now warns that it is the same as plot(x ~ 1, *).
* recordPlot() has new arguments load and attach to allow package
names to be stored as part of a recorded plot. replayPlot() has
new argument reloadPkgs to load/attach any package names that
were stored as part of a recorded plot.
* S4 dispatch works within calls to .Internal(). This means
explicit S4 generics are no longer needed for unlist() and
as.vector().
* Only font family names starting with "Hershey" (and not "Her" as
before) are given special treatment by the graphics engine.
* S4 values are automatically coerced to vector (via as.vector)
when subassigned into atomic vectors.
* findInterval() gets a left.open option.
* The version of LAPACK included in the sources has been updated to
3.6.0, including those 'deprecated' routines which were
previously included. _Ca_ 40 double-complex routines have been
added at the request of a package maintainer.
As before, the details of what is included are in
src/modules/lapack/README and this now gives information on
earlier additions.
* tapply() has been made considerably more efficient without
changing functionality, thanks to proposals from Peter Haverty
and Suharto Anggono. (PR#16640)
* match.arg(arg) (the one-argument case) is faster; so is
sort.int(). (PR#16640)
* The format method for object_size objects now also accepts
"binary" units such as "KiB" and e.g., "Tb". (Partly from
PR#16649.)
* Profiling now records calls of the form foo::bar and some similar
cases directly rather than as calls to <Anonymous>. Contributed
by Winston Chang.
* New string utilities startsWith(x, prefix) and endsWith(x,
suffix). Also provide speedups for some grepl("^...",*) uses
(related to proposals in PR#16490).
* Reference class finalizers run at exit, as well as on garbage
collection.
* Avoid parallel dependency on stats for port choice and random
number seeds. (PR#16668)
* The radix sort algorithm and implementation from data.table
(forder) replaces the previous radix (counting) sort and adds a
new method for order(). Contributed by Matt Dowle and Arun
Srinivasan, the new algorithm supports logical, integer (even
with large values), real, and character vectors. It outperforms
all other methods, but there are some caveats (see ?sort).
* The order() function gains a method argument for choosing between
"shell" and "radix".
* New function grouping() returns a permutation that stably
rearranges data so that identical values are adjacent. The
return value includes extra partitioning information on the
groups. The implementation came included with the new radix
sort.
* rhyper(nn, m, n, k) no longer returns NA when one of the three
parameters exceeds the maximal integer.
* switch() now warns when no alternatives are provided.
* parallel::detectCores() now has default logical = TRUE on all
platforms - as this was the default on Windows, this change only
affects Sparc Solaris.
Option logical = FALSE is now supported on Linux and recent
versions of OS X (for the latter, thanks to a suggestion of Kyaw
Sint).
* hist() for "Date" or "POSIXt" objects would sometimes give
misleading labels on the breaks, as they were set to the day
before the start of the period being displayed. The display
format has been changed, and the shift of the start day has been
made conditional on right = TRUE (the default). (PR#16679)
* R now uses a new version of the logo (donated to the R Foundation
by RStudio). It is defined in .svg format, so will resize
without unnecessary degradation when displayed on HTML
pages-there is also a vector PDF version. Thanks to Dirk
Eddelbuettel for producing the corresponding X11 icon.
* New function .traceback() returns the stack trace which
traceback() prints.
* lengths() dispatches internally.
* dotchart() gains a pt.cex argument to control the size of points
separately from the size of plot labels. Thanks to Michael
Friendly and Milan Bouchet-Valat for ideas and patches.
* as.roman(ch) now correctly deals with more diverse character
vectors ch; also arithmetic with the resulting roman numbers
works in more cases. (PR#16779)
* prcomp() gains a new option rank. allowing to directly aim for
less than min(n,p) PC's. The summary() and its print() method
have been amended, notably for this case.
* gzcon() gains a new option text, which marks the connection as
text-oriented (so e.g. pushBack() works). It is still always
opened in binary mode.
* The import() namespace directive now accepts an argument except
which names symbols to exclude from the imports. The except
expression should evaluate to a character vector (after
substituting symbols for strings). See Writing R Extensions.
* New convenience function Rcmd() in package tools for invoking R
CMD tools from within R.
* New functions makevars_user() and makevars_site() in package
tools to determine the location of the user and site specific
Makevars files for customizing package compilation.
* 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.
/usr/lib64/R/library/boot /usr/lib64/R/library/boot/CITATION /usr/lib64/R/library/boot/DESCRIPTION /usr/lib64/R/library/boot/INDEX /usr/lib64/R/library/boot/Meta /usr/lib64/R/library/boot/Meta/Rd.rds /usr/lib64/R/library/boot/Meta/data.rds /usr/lib64/R/library/boot/Meta/features.rds /usr/lib64/R/library/boot/Meta/hsearch.rds /usr/lib64/R/library/boot/Meta/links.rds /usr/lib64/R/library/boot/Meta/nsInfo.rds /usr/lib64/R/library/boot/Meta/package.rds /usr/lib64/R/library/boot/NAMESPACE /usr/lib64/R/library/boot/R /usr/lib64/R/library/boot/R/boot /usr/lib64/R/library/boot/R/boot.rdb /usr/lib64/R/library/boot/R/boot.rdx /usr/lib64/R/library/boot/bd.q /usr/lib64/R/library/boot/data /usr/lib64/R/library/boot/data/Rdata.rdb /usr/lib64/R/library/boot/data/Rdata.rds /usr/lib64/R/library/boot/data/Rdata.rdx /usr/lib64/R/library/boot/help /usr/lib64/R/library/boot/help/AnIndex /usr/lib64/R/library/boot/help/aliases.rds /usr/lib64/R/library/boot/help/boot.rdb /usr/lib64/R/library/boot/help/boot.rdx /usr/lib64/R/library/boot/help/paths.rds /usr/lib64/R/library/boot/html /usr/lib64/R/library/boot/html/00Index.html /usr/lib64/R/library/boot/html/R.css /usr/lib64/R/library/boot/po /usr/lib64/R/library/boot/po/de /usr/lib64/R/library/boot/po/de/LC_MESSAGES /usr/lib64/R/library/boot/po/de/LC_MESSAGES/R-boot.mo /usr/lib64/R/library/boot/po/en@quot /usr/lib64/R/library/boot/po/en@quot/LC_MESSAGES /usr/lib64/R/library/boot/po/en@quot/LC_MESSAGES/R-boot.mo /usr/lib64/R/library/boot/po/fr /usr/lib64/R/library/boot/po/fr/LC_MESSAGES /usr/lib64/R/library/boot/po/fr/LC_MESSAGES/R-boot.mo /usr/lib64/R/library/boot/po/it /usr/lib64/R/library/boot/po/it/LC_MESSAGES /usr/lib64/R/library/boot/po/it/LC_MESSAGES/R-boot.mo /usr/lib64/R/library/boot/po/ko /usr/lib64/R/library/boot/po/ko/LC_MESSAGES /usr/lib64/R/library/boot/po/ko/LC_MESSAGES/R-boot.mo /usr/lib64/R/library/boot/po/pl /usr/lib64/R/library/boot/po/pl/LC_MESSAGES /usr/lib64/R/library/boot/po/pl/LC_MESSAGES/R-boot.mo /usr/lib64/R/library/boot/po/ru /usr/lib64/R/library/boot/po/ru/LC_MESSAGES /usr/lib64/R/library/boot/po/ru/LC_MESSAGES/R-boot.mo
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Fabrice Bellet, Tue Jul 9 18:17:49 2024