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pkglint -Wall -F --only aligned -r
Manual correction in R/Makefile.extension for the MASTER_SITES
continuation line.
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Upstream changes:
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.
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The category 'R' is used to denote R packages, just as 'perl5' and 'python'
are used in other cases. To ensure consistency, add that to CATEGORIES in
Makefile.extension rather than in each individual R package. This was
discussed in http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html.
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Upstream changes:
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).
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Upstream changes:
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.
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Upstream changes:
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.
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Distfiles for older R packges are moved on CRAN from contrib/ to
contrib/Archive/${R_PKGNAME}/. As a result, they may be inaccessible to
'make fetch'. Add the additional directory to MASTER_SITES in
math/R/Makefile.extension so that older distfiles will be retrieved
directly from CRAN. In addition, remove the definition of MASTER_SITES
from math/R-prob/Makefile, which is the only package directly referring to
the distfile archive. At this point all R packages should rely on
math/R/Makefile.extension to define MASTER_SITES; they should not be
defining MASTER_SITES directly.
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Upstream changes:
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 Hervé Pagès 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.
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Upstream changes:
CHANGES IN R 3.5.0
SIGNIFICANT USER-VISIBLE CHANGES
All packages are by default byte-compiled on installation. This makes the installed packages larger (usually marginally so) and may affect the format of messages and tracebacks (which often exclude .Call and similar).
NEW FEATURES
factor() now uses order() to sort its levels, rather than sort.list(). This allows factor() to support custom vector-like objects if methods for the appropriate generics are defined. It has the side effect of making factor() succeed on empty or length-one non-atomic vector(-like) types (e.g., "list"), where it failed before.
diag() gets an optional names argument: this may require updates to packages defining S4 methods for it.
chooseCRANmirror() and chooseBioCmirror() no longer have a useHTTPS argument, not needed now all R builds support https:// downloads.
New summary() method for warnings() with a (somewhat experimental) print() method.
(methods package.) .self is now automatically registered as a global variable when registering a reference class method.
tempdir(check = TRUE) recreates the tempdir() directory if it is no longer valid (e.g. because some other process has cleaned up the ‘/tmp’ directory).
New askYesNo() function and "askYesNo" option to ask the user binary response questions in a customizable but consistent way. (Suggestion of PR#17242.)
New low level utilities ...elt(n) and ...length() for working with ... parts inside a function.
isTRUE() is more tolerant and now true in
x <- rlnorm(99)
isTRUE(median(x) == quantile(x)["50%"])
New function isFALSE() defined analogously to isTRUE().
The default symbol table size has been increased from 4119 to 49157; this may improve the performance of symbol resolution when many packages are loaded. (Suggested by Jim Hester.)
line() gets a new option iter = 1.
Reading from connections in text mode is buffered, significantly improving the performance of readLines(), as well as scan() and read.table(), at least when specifying colClasses.
order() is smarter about picking a default sort method when its arguments are objects.
available.packages() has two new arguments which control if the values from the per-session repository cache are used (default true, as before) and if so how old cached values can be to be used (default one hour).
These arguments can be passed from install.packages(), update.packages() and functions calling that: to enable this available.packages(), packageStatus() and download.file() gain a ... argument.
packageStatus()'s upgrade() method no longer ignores its ... argument but passes it to install.packages().
installed.packages() gains a ... argument to allow arguments (including noCache) to be passed from new.packages(), old.packages(), update.packages() and packageStatus().
factor(x, levels, labels) now allows duplicated labels (not duplicated levels!). Hence you can map different values of x to the same level directly.
Attempting to use names<-() on an S4 derivative of a basic type no longer emits a warning.
The list method of within() gains an option keepAttrs = FALSE for some speed-up.
system() and system2() now allow the specification of a maximum elapsed time (‘timeout’).
debug() supports debugging of methods on any object of S4 class "genericFunction", including group generics.
Attempting to increase the length of a variable containing NULL using length()<- still has no effect on the target variable, but now triggers a warning.
type.convert() becomes a generic function, with additional methods that operate recursively over list and data.frame objects. Courtesy of Arni Magnusson (PR#17269).
lower.tri(x) and upper.tri(x) only needing dim(x) now work via new functions .row() and .col(), so no longer call as.matrix() by default in order to work efficiently for all kind of matrix-like objects.
print() methods for "xgettext" and "xngettext" now use encodeString() which keeps, e.g. "\n", visible. (Wish of PR#17298.)
package.skeleton() gains an optional encoding argument.
approx(), spline(), splinefun() and approxfun() also work for long vectors.
deparse() and dump() are more useful for S4 objects, dput() now using the same internal C code instead of its previous imperfect workaround R code. S4 objects now typically deparse perfectly, i.e., can be recreated identically from deparsed code.
dput(), deparse() and dump() now print the names() information only once, using the more readable (tag = value) syntax, notably for list()s, i.e., including data frames.
These functions gain a new control option "niceNames" (see .deparseOpts()), which when set (as by default) also uses the (tag = value) syntax for atomic vectors. On the other hand, without deparse options "showAttributes" and "niceNames", names are no longer shown also for lists. as.character(list( c (one = 1))) now includes the name, as as.character(list(list(one = 1))) has always done.
m:n now also deparses nicely when m > n.
The "quoteExpressions" option, also part of "all", no longer quote()s formulas as that may not re-parse identically. (PR#17378)
If the option setWidthOnResize is set and TRUE, R run in a terminal using a recent readline library will set the width option when the terminal is resized. Suggested by Ralf Goertz.
If multiple on.exit() expressions are set using add = TRUE then all expressions will now be run even if one signals an error.
mclapply() gets an option affinity.list which allows more efficient execution with heterogeneous processors, thanks to Helena Kotthaus.
The character methods for as.Date() and as.POSIXlt() are more flexible via new arguments tryFormats and optional: see their help pages.
on.exit() gains an optional argument after with default TRUE. Using after = FALSE with add = TRUE adds an exit expression before any existing ones. This way the expressions are run in a first-in last-out fashion. (From Lionel Henry.)
On Windows, file.rename() internally retries the operation in case of error to attempt to recover from possible anti-virus interference.
Command line completion on :: now also includes lazy-loaded data.
If the TZ environment variable is set when date-time functions are first used, it is recorded as the session default and so will be used rather than the default deduced from the OS if TZ is subsequently unset.
There is now a [ method for class "DLLInfoList".
glm() and glm.fit get the same singular.ok = TRUE argument that lm() has had forever. As a consequence, in glm(*, method = <your_own>), user specified methods need to accept a singular.ok argument as well.
aspell() gains a filter for Markdown (‘.md’ and ‘.Rmd’) files.
intToUtf8(multiple = FALSE) gains an argument to allow surrogate pairs to be interpreted.
The maximum number of DLLs that can be loaded into R e.g. via dyn.load() has been increased up to 614 when the OS limit on the number of open files allows.
Sys.timezone() on a Unix-alike caches the value at first use in a session: inter alia this means that setting TZ later in the session affects only the current time zone and not the system one.
Sys.timezone() is now used to find the system timezone to pass to the code used when R is configured with --with-internal-tzcode.
When tar() is used with an external command which is detected to be GNU tar or libarchive tar (aka bsdtar), a different command-line is generated to circumvent line-length limits in the shell.
system(*, intern = FALSE), system2() (when not capturing output), file.edit() and file.show() now issue a warning when the external command cannot be executed.
The “default” ("lm" etc) methods of vcov() have gained new optional argument complete = TRUE which makes the vcov() methods more consistent with the coef() methods in the case of singular designs. The former (back-compatible) behavior is given by vcov(*, complete = FALSE).
coef() methods (for lm etc) also gain a complete = TRUE optional argument for consistency with vcov().
For "aov", both coef() and vcov() methods remain back-compatibly consistent, using the other default, complete = FALSE.
attach(*, pos = 1) is now an error instead of a warning.
New function getDefaultCluster() in package parallel to get the default cluster set via setDefaultCluster().
str(x) for atomic objects x now treats both cases of is.vector(x) similarly, and hence much less often prints "atomic". This is a slight non-back-compatible change producing typically both more informative and shorter output.
write.dcf() gets optional argument useBytes.
New, partly experimental packageDate() which tries to get a valid "Date" object from a package ‘DESCRIPTION’ file, thanks to suggestions in PR#17324.
tools::resaveRdaFiles() gains a version argument, for use when packages should remain compatible with earlier versions of R.
ar.yw(x) and hence by default ar(x) now work when x has NAs, mostly thanks to a patch by Pavel Krivitsky in PR#17366. The ar.yw.default()'s AIC computations have become more efficient by using determinant().
New warnErrList() utility (from package nlme, improved).
By default the (arbitrary) signs of the loadings from princomp() are chosen so the first element is non-negative.
If --default-packages is not used, then Rscript now checks the environment variable R_SCRIPT_DEFAULT_PACKAGES. If this is set, then it takes precedence over R_DEFAULT_PACKAGES. If default packages are not specified on the command line or by one of these environment variables, then Rscript now uses the same default packages as R. For now, the previous behavior of not including methods can be restored by setting the environment variable R_SCRIPT_LEGACY to yes.
When a package is found more than once, the warning from find.package(*, verbose=TRUE) lists all library locations.
POSIXt objects can now also be rounded or truncated to month or year.
stopifnot() can be used alternatively via new argument exprs which is nicer and useful when testing several expressions in one call.
The environment variable R_MAX_VSIZE can now be used to specify the maximal vector heap size. On macOS, unless specified by this environment variable, the maximal vector heap size is set to the maximum of 16GB and the available physical memory. This is to avoid having the R process killed when macOS over-commits memory.
sum(x) and sum(x1,x2,..,x<N>) with many or long logical or integer vectors no longer overflows (and returns NA with a warning), but returns double numbers in such cases.
Single components of "POSIXlt" objects can now be extracted and replaced via [ indexing with 2 indices.
S3 method lookup now searches the namespace registry after the top level environment of the calling environment.
Arithmetic sequences created by 1:n, seq_along, and the like now use compact internal representations via the ALTREP framework. Coercing integer and numeric vectors to character also now uses the ALTREP framework to defer the actual conversion until first use.
Finalizers are now run with interrupts suspended.
merge() gains new option no.dups and by default suffixes the second of two duplicated column names, thanks to a proposal by Scott Ritchie (and Gabe Becker).
scale.default(x, center, scale) now also allows center or scale to be “numeric-alike”, i.e., such that as.numeric(.) coerces them correctly. This also eliminates a wrong error message in such cases.
par*apply and par*applyLB gain an optional argument chunk.size which allows to specify the granularity of scheduling.
Some as.data.frame() methods, notably the matrix one, are now more careful in not accepting duplicated or NA row names, and by default produce unique non-NA row names. This is based on new function .rowNamesDF(x, make.names = *) <- rNms where the logical argument make.names allows to specify how invalid row names rNms are handled. .rowNamesDF() is a “workaround” compatible default.
R has new serialization format (version 3) which supports custom serialization of ALTREP framework objects. These objects can still be serialized in format 2, but less efficiently. Serialization format 3 also records the current native encoding of unflagged strings and converts them when de-serialized in R running under different native encoding. Format 3 comes with new serialization magic numbers (RDA3, RDB3, RDX3). Format 3 can be selected by version = 3 in save(), serialize() and saveRDS(), but format 2 remains the default for all serialization and saving of the workspace. Serialized data in format 3 cannot be read by versions of R prior to version 3.5.0.
The "Date" and “date-time” classes "POSIXlt" and "POSIXct" now have a working `length<-` method, as wished in PR#17387.
optim(*, control = list(warn.1d.NelderMead = FALSE)) allows to turn off the warning when applying the default "Nelder-Mead" method to 1-dimensional problems.
matplot(.., panel.first = .) etc now work, as log becomes explicit argument and ... is passed to plot() unevaluated, as suggested by Sebastian Meyer in PR#17386.
Interrupts can be suspended while evaluating an expression using suspendInterrupts. Subexpression can be evaluated with interrupts enabled using allowInterrupts. These functions can be used to make sure cleanup handlers cannot be interrupted.
R 3.5.0 includes a framework that allows packages to provide alternate representations of basic R objects (ALTREP). The framework is still experimental and may undergo changes in future R releases as more experience is gained. For now, documentation is provided in https://svn.r-project.org/R/branches/ALTREP/ALTREP.html.
UTILITIES
install.packages() for source packages now has the possibility to set a ‘timeout’ (elapsed-time limit). For serial installs this uses the timeout argument of system2(): for parallel installs it requires the timeout utility command from GNU coreutils.
It is now possible to set ‘timeouts’ (elapsed-time limits) for most parts of R CMD check via environment variables documented in the ‘R Internals’ manual.
The ‘BioC extra’ repository which was dropped from Bioconductor 3.6 and later has been removed from setRepositories(). This changes the mapping for 6–8 used by setRepositories(ind=).
R CMD check now also applies the settings of environment variables _R_CHECK_SUGGESTS_ONLY_ and _R_CHECK_DEPENDS_ONLY_ to the re-building of vignettes.
R CMD check with environment variable _R_CHECK_DEPENDS_ONLY_ set to a true value makes test-suite-management packages available and (for the time being) works around a common omission of rmarkdown from the VignetteBuilder field.
INSTALLATION on a UNIX-ALIKE
Support for a system Java on macOS has been removed — install a fairly recent Oracle Java (see ‘R Installation and Administration’ §C.3.2).
configure works harder to set additional flags in SAFE_FFLAGS only where necessary, and to use flags which have little or no effect on performance.
In rare circumstances it may be necessary to override the setting of SAFE_FFLAGS.
C99 functions expm1, hypot, log1p and nearbyint are now required.
configure sets a -std flag for the C++ compiler for all supported C++ standards (e.g., -std=gnu++11 for the C++11 compiler). Previously this was not done in a few cases where the default standard passed the tests made (e.g. clang 6.0.0 for C++11).
C-LEVEL FACILITIES
‘Writing R Extensions’ documents macros MAYBE_REFERENCED, MAYBE_SHARED and MARK_NOT_MUTABLE that should be used by package C code instead NAMED or SET_NAMED.
The object header layout has been changed to support merging the ALTREP branch. This requires re-installing packages that use compiled code.
‘Writing R Extensions’ now documents the R_tryCatch, R_tryCatchError, and R_UnwindProtect functions.
NAMEDMAX has been raised to 3 to allow protection of intermediate results from (usually ill-advised) assignments in arguments to BUILTIN functions. Package C code using SET_NAMED may need to be revised.
DEPRECATED AND DEFUNCT
Sys.timezone(location = FALSE) is defunct, and is ignored (with a warning).
methods:::bind_activation() is defunct now; it typically has been unneeded for years.
The undocumented ‘hidden’ objects .__H__.cbind and .__H__.rbind in package base are deprecated (in favour of cbind and rbind).
The declaration of pythag() in ‘Rmath.h’ has been removed — the entry point has not been provided since R 2.14.0.
BUG FIXES
printCoefmat() now also works without column names.
The S4 methods on Ops() for the "structure" class no longer cause infinite recursion when the structure is not an S4 object.
nlm(f, ..) for the case where f() has a "hessian" attribute now computes LL' = H + µI correctly. (PR#17249).
An S4 method that “rematches” to its generic and overrides the default value of a generic formal argument to NULL no longer drops the argument from its formals.
Rscript can now accept more than one argument given on the #! line of a script. Previously, one could only pass a single argument on the #! line in Linux.
Connections are now written correctly with encoding "UTF-16LE". (PR#16737).
Evaluation of ..0 now signals an error. When ..1 is used and ... is empty, the error message is more appropriate.
(Windows mainly.) Unicode code points which require surrogate pairs in UTF-16 are now handled. All systems should properly handle surrogate pairs, even those systems that do not need to make use of them. (PR#16098)
stopifnot(e, e2, ...) now evaluates the expressions sequentially and in case of an error or warning shows the relevant expression instead of the full stopifnot(..) call.
path.expand() on Windows now accepts paths specified as UTF-8-encoded character strings even if not representable in the current locale. (PR#17120)
line(x, y) now correctly computes the medians of the left and right group's x-values and in all cases reproduces straight lines.
Extending S4 classes with slots corresponding to special attributes like dim and dimnames now works.
Fix for legend() when fill has multiple values the first of which is NA (all colours used to default to par(fg)). (PR#17288)
installed.packages() did not remove the cached value for a library tree that had been emptied (but would not use the old value, just waste time checking it).
The documentation for installed.packages(noCache = TRUE) incorrectly claimed it would refresh the cache.
aggregate(<data.frame>) no longer uses spurious names in some cases. (PR#17283)
object.size() now also works for long vectors.
packageDescription() tries harder to solve re-encoding issues, notably seen in some Windows locales. This fixes the citation() issue in PR#17291.
poly(<matrix>, 3) now works, thanks to prompting by Marc Schwartz.
readLines() no longer segfaults on very large files with embedded '\0' (aka ‘nul’) characters. (PR#17311)
ns() (package splines) now also works for a single observation. interpSpline() gives a more friendly error message when the number of points is less than four.
dist(x, method = "canberra") now uses the correct definition; the result may only differ when x contains values of differing signs, e.g. not for 0-1 data.
methods:::cbind() and methods:::rbind() avoid deep recursion, thanks to Suharto Anggono via PR#17300.
Arithmetic with zero-column data frames now works more consistently; issue raised by Bill Dunlap.
Arithmetic with data frames gives a data frame for ^ (which previously gave a numeric matrix).
pretty(x, n) for large n or large diff(range(x)) now works better (though it was never meant for large n); internally it uses the same rounding fuzz (1e-10) as seq.default() — as it did up to 2010-02-03 when both were 1e-7.
Internal C-level R_check_class_and_super() and hence R_check_class_etc() now also consider non-direct super classes and hence return a match in more cases. This e.g., fixes behaviour of derived classes in package Matrix.
Reverted unintended change in behavior of return calls in on.exit expressions introduced by stack unwinding changes in R 3.3.0.
Attributes on symbols are now detected and prevented; attempt to add an attribute to a symbol results in an error.
fisher.test(*, workspace = <n>) now may also increase the internal stack size which allows larger problem to be solved, fixing PR#1662.
The methods package no longer directly copies slots (attributes) into a prototype that is of an “abnormal” (reference) type, like a symbol.
The methods package no longer attempts to call length<-() on NULL (during the bootstrap process).
The methods package correctly shows methods when there are multiple methods with the same signature for the same generic (still not fully supported, but at least the user can see them).
sys.on.exit() is now always evaluated in the right frame. (From Lionel Henry.)
seq.POSIXt(*, by = "<n> DSTdays") now should work correctly in all cases and is faster. (PR#17342)
.C() when returning a logical vector now always maps values other than FALSE and NA to TRUE (as documented).
Subassignment with zero length vectors now coerces as documented (PR#17344).
Further, x <- numeric(); x[1] <- character() now signals an error ‘replacement has length zero’ (or a translation of that) instead of doing nothing.
(Package parallel.) mclapply(), pvec() and mcparallel() (when mccollect() is used to collect results) no longer leave zombie processes behind.
R CMD INSTALL <pkg> now produces the intended error message when, e.g., the LazyData field is invalid.
as.matrix(dd) now works when the data frame dd contains a column which is a data frame or matrix, including a 0-column matrix/d.f. .
mclapply(X, mc.cores) now follows its documentation and calls lapply() in case mc.cores = 1 also in the case mc.preschedule is false. (PR#17373)
aggregate(<data.frame>, drop=FALSE) no longer calls the function on <empty> parts but sets corresponding results to NA. (Thanks to Suharto Anggono's patches in PR#17280).
The duplicated() method for data frames is now based on the list method (instead of string coercion). Consequently unique() is better distinguishing data frame rows, fixing PR#17369 and PR#17381. The methods for matrices and arrays are changed accordingly.
Calling names() on an S4 object derived from "environment" behaves (by default) like calling names() on an ordinary environment.
read.table() with a non-default separator now supports quotes following a non-whitespace character, matching the behavior of scan().
parLapplyLB and parSapplyLB have been fixed to do load balancing (dynamic scheduling). This also means that results of computations depending on random number generators will now really be non-reproducible, as documented.
Indexing a list using dollar and empty string (l$"") returns NULL.
Using \usage{ data(<name>, package="<pkg>") } no longer produces R CMD check warnings.
match.arg() more carefully chooses the environment for constructing default choices, fixing PR#17401 as proposed by Duncan Murdoch.
Deparsing of consecutive ! calls is now consistent with deparsing unary - and + calls and creates code that can be reparsed exactly; thanks to a patch by Lionel Henry in PR#17397. (As a side effect, this uses fewer parentheses in some other deparsing involving ! calls.)
[R logo] CHANGES IN R 3.4.4
NEW FEATURES
Sys.timezone() tries more heuristics on Unix-alikes and so is more likely to succeed (especially on Linux). For the slowest method, a warning is given recommending that TZ is set to avoid the search.
The version of LAPACK included in the sources has been updated to 3.8.0 (for the routines used by R, a very minor bug-fix change).
parallel::detectCores(logical = FALSE) is ignored on Linux systems, since the information is not available with virtualized OSes.
INSTALLATION on a UNIX-ALIKE
configure will use pkg-config to find the flags to link to jpeg if available (as it should be for the recently-released jpeg-9c and libjpeg-turbo). (This amends the code added in R 3.3.0 as the module name in jpeg-9c is not what that tested for.)
DEPRECATED AND DEFUNCT
Sys.timezone(location = FALSE) (which was a stop-gap measure for Windows long ago) is deprecated. It no longer returns the value of environment variable TZ (usually a location).
Legacy support of make macros such as CXX1X is formally deprecated: use the CXX11 forms instead.
BUG FIXES
power.prop.test() now warns when it cannot solve the problem, typically because of impossible constraints. (PR#17345)
removeSource() no longer erroneously removes NULL in certain cases, thanks to Dénes Tóth.
nls(`NO [mol/l]` ~ f(t)) and nls(y ~ a) now work. (Partly from PR#17367)
R CMD build checks for GNU cp rather than assuming Linux has it. (PR#17370 says ‘Alpine Linux’ does not.)
Non-UTF-8 multibyte character handling fixed more permanently (PR#16732).
sum(<large ints>, <stuff>) is more consistent. (PR#17372)
rf() and rbeta() now also work correctly when ncp is not scalar, notably when (partly) NA. (PR#17375)
is.na(NULL) no longer warns. (PR#16107)
R CMD INSTALL now correctly sets C++ compiler flags when all source files are in sub-directories of ‘src’.
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This reduces # of variables to define in an R extension package.
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This package was already using libblas from the Accelerate framework
on Darwin through /usr/lib/libblas.dylib. This change makes it
explicit and removes unnecessary dependencies on math/blas and
math/lapack.
Bump PKGREVISION.
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The actual fix as been done by "pkglint -F */*/buildlink3.mk", and was
reviewed manually.
There are some .include lines that still are indented with zero spaces
although the surrounding .if is indented. This is existing practice.
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Upstream changes:
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.
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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)
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.
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.)
And many more - see the NEWS file for details.
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PkgSrc changes:
* On Darwin, use Aqua interface instead of X11
* Cairo support also requires Pango
* Allow Cairo with other backends, not only X11 (e.g. to make it work on Darwin)
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Also move fixes from configure to configure.ac
m4/R.m4 fix by @joerg
Oked @joerg
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cpow and clog are not implemented on FreeBSD and the configure checks only
emit warnings instead of errors.
Ok@ markd
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Upstream 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 §8 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).
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Upstream 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.)
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