This blog is updated daily.
A general description is here.
‘type.convert()’ (and hence ‘read.table(as.is = TRUE)’) returns a character vector or factor when representing a numeric input as a double would lose accuracy. Similarly for complex inputs.
If a file contains numeric data with unrepresentable numbers of decimal places that are intended to be read as numeric, specify ‘colClasses’ in ‘read.table()’ to be ‘"numeric"’.
‘tools::Rdiff(useDiff = FALSE)’ is closer to the POSIX definition of ‘diff -b’ (as distinct from the description in the ‘man’ pages of most systems).
New function ‘anyNA()’, a fast version of ‘any(is.na(.))’, _where neither ‘is.na()’ nor ‘any()’ has a relevant method_, based on a proposal by Tim Hesterberg. (Wish of PR#15239.)
‘arrayInd(*, useNames = TRUE)’ and, analogously, ‘which(*, arr.ind = TRUE)’ now make use of ‘names(.dimnames)’ when available.
‘is.unsorted()’ now also works for ‘raw’ vectors.
The ‘"table"’ method for ‘as.data.frame()’ (also useful as ‘as.data.frame.table()’) now passes ‘sep’ and ‘base’ arguments to ‘provideDimnames()’.
‘uniroot()’ gets new optional arguments, notably ‘extendInt’, allowing to auto-extend the search interval when needed. The return value has an extra component, ‘init.it’.
‘switch(f, ...)’ now warns when ‘f’ is a factor, as this typically happens accidentally where the useR meant to pass a character string, but ‘f’ is treated as integer (as always documented).
The parser has been modified to use less memory.
The way the unary operators (‘+ - !’) handle attributes is now more consistent. If there is no coercion, all attributes (including class) are copied from the input to the result: otherwise only names, dims and dimnames are.
‘colorRamp()’ and ‘colorRampPalette()’ now allow non-opaque colours and a ramp in opacity via the new argument ‘alpha = TRUE’. (Suggested by Alberto Krone-Martins, but optionally as there are existing uses which expect only RGB values.)
‘grid.show.layout()’ and ‘grid.show.viewport()’ get an optional ‘vp.ex’ argument.
There is a new function ‘find_gs_cmd()’ in the ‘tools’ package to locate a GhostScript executable. (This is an enhanced version of a previously internal function there.)
‘object.size()’ gains a ‘format()’ method.
There is a new family, ‘"ArialMT"’, for the ‘pdf()’ and ‘postscript()’ devices. This will only be rendered correctly on viewers which have access to Monotype TrueType fonts (which are sometimes requested by journals).
The text and PDF news files, including ‘NEWS’ and ‘NEWS.2’, have been moved to the ‘doc’ directory.
‘combn(x, simplify = TRUE)’ now gives a factor result for factor input ‘x’ (previously user error). (Related to PR#15442.)
Added ‘utils::fileSnapshot()’ and ‘utils::changedFiles()’ functions to allow snapshots and comparison of directories of files.
‘make.names(names, unique=TRUE)’ now tries to preserve existing names. (Suggestion of PR#15452.)
New functions ‘cospi(x)’, ‘sinpi(x)’, and ‘tanpi(x)’, for more accurate computation of ‘cos(pi*x)’, etc, both in R and the C API. Using these gains accuracy in some cases, e.g., inside ‘lgamma()’ or ‘besselI()’. (Suggested by Morten Welinder in PR#15529.)
‘print.table(x, zero.print = ".")’ now also has an effect when ‘x’ is not integer-valued.
There is more support to explore the system's idea of time-zone names. ‘Sys.timezone()’ tries to give the current system setting by name (and succeeds at least on Linux, OS X, Solaris and Windows), and ‘OlsonNames()’ lists the names in the system's Olson database. ‘Sys.timezone(location = FALSE)’ gives the previous behaviour.
Platforms with a 64-bit ‘time_t’ type are allowed to handle conversions between the ‘"POSIXct"’ and ‘"POSIXlt"’ classes for date-times outside the 32-bit range (before 1902 or after 2037): the existing workarounds are used on other platforms. (Note that time-zone information for post-2037 is speculative at best, and the OS services are tested for known errors and so not used on OS X.)
Currently ‘time_t’ is usually ‘long’ and hence 64-bit on Unix-alike 64-bit platforms: however it several cases the time-zone database is 32-bit. On R for Windows it is 64-bit (for both architectures as from this version).
The ‘"save.defaults"’ option can include a value for ‘compression_level’. (Wish of PR#15579.)
‘colSums()’ and friends now have support for arrays and data-frame columns with 2^31 or more elements.
‘as.factor()’ is faster when ‘f’ is an unclassed integer vector (for example, when called from ‘tapply()’).
‘fft()’ now works with longer inputs, from the 12 million previously supported up to 2 billion. (PR#15593)
Complex ‘svd()’ now uses LAPACK subroutine ‘ZGESDD’, the complex analogue of the routine used for the real case.
Sweave now outputs ‘.tex’ files in UTF-8 if the input encoding is declared to be UTF-8, regardless of the local encoding. The UTF-8 encoding may now be declared using a LaTeX comment containing the string ‘%\SweaveUTF8’ on a line by itself.
‘file.copy()’ gains a ‘copy.date’ argument.
Printing of date-times will make use of the time-zone abbreviation in use at the time, if known. For example, for Paris pre-1940 this could be ‘LMT’, ‘PMT’, ‘WET’ or ‘WEST’. To enable this, the ‘"POSIXlt"’ class has an optional component ‘"zone"’ recording the abbreviation for each element.
For platforms which support it, there is also a component ‘"gmtoff"’ recording the offset from GMT where known.
(On Windows, by default on OS X and optionally elsewhere.) The system C function ‘strftime’ has been replaced by a more comprehensive version with closer conformance to the POSIX 2008 standard.
‘dnorm(x, log = FALSE)’ is more accurate (but somewhat slower) for |x| > 5; as suggested in PR#15620.
Some versions of the ‘tiff()’ device have further compression options.
‘read.table()’, ‘readLines()’ and ‘scan()’ have a new argument to influence the treatment of embedded nuls.
Avoid duplicating the right hand side values in complex assignments when possible. This reduces copying of replacement values in expressions such as ‘Z$a <- a0’ and ‘ans[[i]] <- tmp’: some package code has relied on there being copies. (Based on suggestions from Michael Lawrence.)
The ‘fast’ argument of ‘KalmanLike()’, ‘KalmanRun()’ and ‘KalmanForecast()’ has been replaced by ‘update’, which instead of updating ‘mod’ in place, optionally returns the updated model in an attribute ‘"mod"’ of the return value.
‘arima()’ and ‘makeARIMA()’ get a new optional argument ‘SSinit’, allowing the choice of a different *s*tate *s*pace initialization which has been observed to be more reliable close to non-stationarity: see PR#14682.
‘warning()’ has a new argument ‘noBreaks.’, to simplify post-processing of output with ‘options(warn = 1)’.
‘pushBack()’ gains an argument ‘encoding’, to support reading of UTF-8 characters using ‘scan()’, ‘read.table()’ and related functions in a non-UTF-8 locale.
‘all.equal.list()’ gets a new argument ‘use.names’ which by default labels differing components by names (if they match) rather than by integer index. Saved R output in packages may need to be updated.
The methods for ‘all.equal()’ and ‘attr.all.equal()’ now have argument ‘check.attributes’ after ‘...’ so it cannot be partially nor positionally matched (as it has been, unintentionally).
A side effect is that some previously undetected errors of passing empty arguments (no object between commas) to ‘all.equal()’ are detected and reported.
There are explicit checks that ‘check.attributes’ is logical, ‘tolerance’ is numeric and ‘scale’ is ‘NULL’ or numeric. This catches some unintended positional matching.
The message for ‘all.equal.numeric()’ reports a ‘"scaled difference"’ only for ‘scale != 1’.
‘all.equal()’ now has a ‘"POSIXt"’ method replacing the ‘"POSIXct"’ method.
The ‘"Date"’ and ‘"POSIXt"’ methods of ‘seq()’ allows ‘by = "quarter"’ for completeness (‘by = "3 months"’ always worked).
A number of changes to reduce copying of objects, contributed by Michael Lawrence.
‘file.path()’ removes any trailing separator on Windows, where they are invalid (although sometimes accepted). This is intended to enhance the portability of code written by those using POSIX file systems (where a trailing ‘/’ can be used to confine path matching to directories).
New function ‘agrepl()’ which like ‘grepl()’ returns a logical vector.
‘fifo()’ is now supported on Windows. (PR#15600)
‘sort.list(method = "radix")’ now allows negative integers (wish of PR#15644).
Some functionality of ‘print.ts()’ is now available in ‘.preformat.ts()’ for more modularity.
‘mcparallel()’ gains an option ‘detach=TRUE’ which allows to execute code independently of the current session. It is based on a new ‘estranged=TRUE’ argument to ‘mcfork()’ which forks child processes such that they become independent of the parent process.
The ‘pdf()’ device omits entirely circles and text at extremely small sizes, since some viewers were failing on such files.
The included version of LAPACK has been updated to 3.5.0.
There is some support for parallel testing of an installation, by setting ‘TEST_MC_CORES’ to an integer greater than one to indicate the maximum number of cores to be used in parallel. (It is worth specifying at least 8 cores if available.) Most of these require a ‘make’ program (such as GNU ‘make’ and ‘dmake’) which supports the ‘$MAKE -j nproc’ syntax.
Except on Windows: the tests of standard package examples in ‘make check’ are done in parallel. This also applies to running ‘tools::testInstalledPackages()’.
The more time-consuming regression tests are done in parallel.
The package checks in ‘make check-devel’ and ‘make check-recommended’ are done in parallel.
More of ‘make check’ will work if recommended packages are not installed: but recommended packages remain needed for thorough checking of an R build.
The version of ‘tzcode’ included in ‘src/extra/tzone’ has been updated. (Formerly used only on Windows.)
The included (64-bit) time-zone conversion code and Olson time-zone database can be used instead of the system version: use ‘configure’ option ‘--with-internal-tzcode’. This is the default on Windows and OS X.
(It might be necessary to set environment variable ‘TZ’ on OSes where this is not already set, although the system timezone is deduced correctly on at least Linux, OS X and Windows.)
This option also switches to the version of ‘strftime’ included in directory ‘src/extra/tzone’.
‘configure’ now tests for a C++11-compliant compiler by testing some basic features. This by default tries flags for the compiler specified by ‘CXX’, but an alternative compiler, options and standard can be specified by variables ‘CXX1X’, ‘CXX1XFLAGS’ and ‘CXX1XSTD’ (e.g. ‘-std=gnu++11’).
R can now optionally be compiled to use reference counting instead of the ‘NAMED’ mechanism by defining ‘SWITCH_TO_REFCNT’ in ‘Rinternals.h’. This may become the default in the future.
There is a new option ‘--use-system-tre’ to use a suitable system ‘tre’ library: at present this means a version from their ‘git’ repository, after corrections. (Wish of PR#15660.)
The ‘CRANextra’ repository is no longer a default repository on Windows: all the binary versions of packages from CRAN are now on CRAN, although ‘CRANextra’ contains packages from Omegahat and elsewhere used by CRAN packages.
Only vignettes sources in directory ‘vignettes’ are considered to be vignettes and hence indexed as such.
In the ‘DESCRIPTION’ file,
License: X11
is no longer recognized as valid. Use ‘MIT’ or ‘BSD_2_clause’ instead, both of which need ‘+ file LICENSE’.
For consistency, entries in ‘.Rinstignore’ are now matched case-insensitively on all platforms.
Help for S4 methods with very long signatures now tries harder to split the description in the ‘Usage’ field to no more than 80 characters per line (some packages had over 120 characters).
‘R CMD INSTALL --build’ (not Windows) now defaults to the internal ‘tar()’ unless ‘R_INSTALL_TAR’ is set.
There is support for compiling C++11 code in packages on suitable platforms: see ‘Writing R Extensions’.
Fake installs now install the contents of directory ‘inst’: some packages use this to install e.g. C++ headers for use by other packages that are independent of the package itself. Option ‘--no-inst’ can be used to get the previous behaviour.
The behaviour of the code browser has been made more consistent, in part following the suggestions in PR#14985.
Calls to ‘browser()’ are now consistent with calls to the browser triggered by ‘debug()’, in that ‘Enter’ will default to ‘n’ rather than ‘c’.
A new browser command ‘s’ has been added, to “step into” function calls.
A new browser command ‘f’ has been added, to “finish” the current loop or function.
Within the browser, the command ‘help’ will display a short list of available commands.
Only vignettes sources in directory ‘vignettes’ are considered to be vignettes by ‘R CMD check’. That has been the preferred location since R 2.14.0 and is now obligatory.
For consistency, ‘R CMD build’ now matches entries in ‘.Rbuildignore’ and ‘vignettes/.install_extras’ case-insensitively on all platforms (not just on Windows).
‘checkFF()’ (called by ‘R CMD check’ by default) can optionally check foreign function calls for consistency with the registered type and argument count. This is the default for ‘R CMD check --as-cran’ or can be enabled by setting environment variable ‘_R_CHECK_FF_CALLS_’ to ‘registration’ (but is in any case suppressed by ‘--install=no’). Because this checks calls in which ‘.NAME’ is an R object and not just a literal character string, some other problems are detected for such calls.
Functions ‘suppressForeignCheck()’ and ‘dontCheck()’ have been added to allow package authors to suppress false positive reports.
‘R CMD check --as-cran’ warns about a false value of the ‘DESCRIPTION’ field ‘BuildVignettes’ for Open Source packages, and ignores it. (An Open Source package needs to have complete sources for its vignettes which should be usable on a suitably well-equipped system).
‘R CMD check --no-rebuild-vignettes’ is defunct: ‘R CMD check --no-build-vignettes’ has been preferred since R 3.0.0.
‘R CMD build --no-vignettes’ is defunct: ‘R CMD build --no-build-vignettes’ has been preferred since R 3.0.0.
‘R CMD Sweave’ and ‘R CMD Stangle’ now process both Sweave and non-Sweave vignettes. The ‘tools::buildVignette()’ function has been added to do the same tasks from within R.
The flags returned by ‘R CMD config --ldflags’ and (where installed) ‘pkg-config --libs libR’ are now those needed to link a front-end against the (shared or static) R library.
‘Sweave.sty’ has a new option ‘[inconsolata]’.
‘R CMD check’ customizations such as ‘_R_CHECK_DEPENDS_ONLY_’ make available packages only in ‘LinkingTo’ only for installation, and not for loading/runtime tests.
‘tools::checkFF()’ reports on ‘.C’ and ‘.Fortran’ calls with ‘DUP = FALSE’ if argument ‘check_DUP’ is true. This is selected by ‘R CMD check’ by default.
‘R CMD check --use-gct’ can be tuned to garbage-collect less frequently using ‘gctorture2()’ _via_ the setting of environment variable ‘_R_CHECK_GCT_N_’.
Where supported, ‘tools::texi2dvi()’ limits the number of passes tried to 20.
(Windows only) A function ‘R_WaitEvent()’ has been added (with declaration in header‘R.h’) to block execution until the next event is received by R.
Remapping in the ‘Rmath.h’ header can be suppressed by defining ‘R_NO_REMAP_RMATH’.
The remapping of ‘rround()’ in header ‘Rmath.h’ has been removed: use ‘fround()’ instead.
‘ftrunc()’ in header ‘Rmath.h’ is now a wrapper for the C99 function ‘trunc()’, which might as well be used in C code: ‘ftrunc()’ is still needed for portable C++ code.
The never-documented remapping of ‘prec()’ to ‘fprec()’ in header ‘Rmath.h’ has been removed.
The included LAPACK subset now contains ‘ZGESDD’ and ‘ZGELSD’.
The function ‘LENGTH()’ now checks that it is only applied to vector arguments. However, in packages ‘length()’ should be used. (In R itself ‘LENGTH()’ is a macro without the function overhead of ‘length()’.)
Calls to ‘SET_VECTOR_ELT()’ and ‘SET_STRING_ELT()’ are now checked for indices which are in-range: several packages were writing one element beyond the allocated length.
‘allocVector3’ has been added which allows custom allocators to be used for individual vector allocations.
‘chol(pivot = TRUE, LINPACK = TRUE)’ is defunct.
Arguments ‘EISPACK’ for ‘eigen()’ and ‘LINPACK’ for ‘chol()’, ‘chol2inv()’, ‘solve()’ and ‘svd()’ are ignored: LAPACK is always used.
‘.find.package()’ and ‘.path.package()’ are defunct: only the versions without the initial dot introduced in R 2.13.0 have ever been in the API.
Partial matching when using the ‘$’ operator _on data frames_ now throws a warning and may become defunct in the future. If partial matching is intended, replace ‘foo$bar’ by ‘foo[["bar", exact = FALSE]]’.
The long-deprecated use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’ files has been removed: such sections are now ignored (with a warning).
‘package.skeleton()’'s deprecated argument ‘namespace’ has been removed.
Many methods are no longer exported by package ‘stats’. They are all registered on their generic, which should be called rather than calling a method directly.
Functions ‘readNEWS()’ and ‘checkNEWS()’ in package ‘tools’ are defunct.
‘download.file(method = "lynx")’ is deprecated.
‘.C(DUP = FALSE)’ and ‘.Fortran(DUP = FALSE)’ are now deprecated, and may be disabled in future versions of R. As their help has long said, ‘.Call()’ is much preferred.
‘R CMD check’ notes such usages (by default).
Calling ‘lm.wfit()’ with no non-zero weights gave an array-overrun in the Fortran code and a not very sensible answer. It is now special-cased with a simpler answer (no ‘qr’ component).
Error messages involving non-syntactic names (e.g. as produced by ‘`\r`’ when that object does not exist) now encode the control characters. (Reported by Hadley Wickham.)
‘getGraphicsEvent()’ caused 100% usage of one CPU in Windows. (PR#15500)
‘nls()’ with no ‘start’ argument may now work inside another function (scoping issue).
‘pbeta()’ and similar work better for very large (billions) ‘ncp’.
Where time zones have changed abbreviations over the years, the software tries to more consistently use the abbreviation appropriate to the time or if that is unknown, the current abbreviation. On some platforms where the C function ‘localtime’ changed the ‘tzname’ variables the reported abbreviation could have been that of the last time converted.
‘all.equal(list(1), identity)’ now works.
Bug fix for pushing viewports in ‘grid’ (reported by JJ Allaire and Kevin Ushey).
NOTE for anyone poking around within the graphics engine display list (despite the warnings not to) that this changes what is recorded by ‘grid’ on the graphics engine display list.
Extra checks have been added for unit resolution and conversion in ‘grid’, to catch instances of division-by-zero. This may introduce error messages in existing code and/or produce a different result in existing code (but only where a non-finite location or dimension may now become zero).
Some bugs in TRE have been corrected by updating from the ‘git’ repository. This allows R to be installed on some platforms for which this was a blocker (PR#15087 suggests Linux on ARM and HP-UX).
‘?’ applied to a call to an S4 generic failed in several cases. (PR#15680)
The implicit S4 generics for primitives with ‘...’ in their argument list were incorrect. (PR#15690)
Bug fixes to ‘methods::callGeneric()’. (PR#15691)
The bug fix to ‘aggregrate()’ in PR#15004 introduced a new bug in the case of no grouping variables. (PR#15699)
In rare cases printing deeply nested lists overran a buffer by one byte and on a few platforms segfaulted. (PR#15679)
The dendrogram method of ‘as.dendrogram()’ was hidden accidentally, (PR#15703), and ‘order.dendrogram(d)’ gave too much for a leaf ‘d’. (PR#15702)
R would try to kill processes on exit that have pids ever used by a child process spawned by ‘mcparallel’ even though the current process with that pid was not actually its child.
‘cophenetic()’ applied to a ‘"dendrogram"’ object sometimes incorrectly returned a ‘"Labels"’ attribute with dimensions. (PR#15706)
‘printCoefmat()’ called from quite a few ‘print()’ methods now obeys small ‘getOption("width")’ settings, line wrapping the ‘"signif. codes"’ legend appropriately. (PR#15708)
The included version of LAPACK has been updated to 3.5.0.
There is some support for parallel testing of an installation, by
setting ‘TEST_MC_CORES’ to an integer greater than one to indicate the
maximum number of cores to be used in parallel. (It is worth specifying
at least 8 cores if available.) Most of these require a ‘make’ program
(such as GNU ‘make’ and ‘dmake’) which supports the ‘$MAKE -j nproc’
syntax.
Except on Windows: the tests of standard package examples in ‘make check’ are done in parallel. This also applies to running ‘tools::testInstalledPackages()’.
The more time-consuming regression tests are done in parallel.
The package checks in ‘make check-devel’ and ‘make check-recommended’ are done in parallel.
More of ‘make check’ will work if recommended packages are not
installed: but recommended packages remain needed for thorough checking
of an R build.
The version of ‘tzcode’ included in ‘src/extra/tzone’ has been updated.
(Formerly used only on Windows.)
The included (64-bit) time-zone conversion code and Olson time-zone
database can be used instead of the system version: use ‘configure’
option ‘--with-internal-tzcode’. This is the default on Windows and OS
X.
(It might be necessary to set environment variable ‘TZ’ on OSes where this is not already set, although the system timezone is deduced correctly on at least Linux, OS X and Windows.)
This option also switches to the version of ‘strftime’ included in directory ‘src/extra/tzone’.
‘configure’ now tests for a C++11-compliant compiler by testing some
basic features. This by default tries flags for the compiler specified
by ‘CXX’, but an alternative compiler, options and standard can be
specified by variables ‘CXX1X’, ‘CXX1XFLAGS’ and ‘CXX1XSTD’ (e.g.
‘-std=gnu++11’).
R can now optionally be compiled to use reference counting instead of
the ‘NAMED’ mechanism by defining ‘SWITCH_TO_REFCNT’ in ‘Rinternals.h’.
This may become the default in the future.
There is a new option ‘--use-system-tre’ to use a suitable system ‘tre’
library: at present this means a version from their ‘git’ repository,
after corrections. (Wish of PR#15660.)
The ‘CRANextra’ repository is no longer a default repository on
Windows: all the binary versions of packages from CRAN are now on CRAN,
although ‘CRANextra’ contains packages from Omegahat and elsewhere used
by CRAN packages.
Only vignettes sources in directory ‘vignettes’ are considered to be
vignettes and hence indexed as such.
In the ‘DESCRIPTION’ file,
License: X11
is no longer recognized as valid. Use ‘MIT’ or ‘BSD_2_clause’ instead, both of which need ‘+ file LICENSE’.
For consistency, entries in ‘.Rinstignore’ are now matched
case-insensitively on all platforms.
Help for S4 methods with very long signatures now tries harder to split
the description in the ‘Usage’ field to no more than 80 characters per
line (some packages had over 120 characters).
‘R CMD INSTALL --build’ (not Windows) now defaults to the internal
‘tar()’ unless ‘R_INSTALL_TAR’ is set.
There is support for compiling C++11 code in packages on suitable
platforms: see ‘Writing R Extensions’.
Fake installs now install the contents of directory ‘inst’: some
packages use this to install e.g. C++ headers for use by other packages
that are independent of the package itself. Option ‘--no-inst’ can be
used to get the previous behaviour.
The behaviour of the code browser has been made more consistent, in
part following the suggestions in PR#14985.
Calls to ‘browser()’ are now consistent with calls to the browser
triggered by ‘debug()’, in that ‘Enter’ will default to ‘n’ rather than
‘c’.
A new browser command ‘s’ has been added, to “step into” function
calls.
A new browser command ‘f’ has been added, to “finish” the current loop
or function.
Within the browser, the command ‘help’ will display a short list of
available commands.
Only vignettes sources in directory ‘vignettes’ are considered to be
vignettes by ‘R CMD check’. That has been the preferred location since
R 2.14.0 and is now obligatory.
For consistency, ‘R CMD build’ now matches entries in ‘.Rbuildignore’
and ‘vignettes/.install_extras’ case-insensitively on all platforms
(not just on Windows).
‘checkFF()’ (called by ‘R CMD check’ by default) can optionally check
foreign function calls for consistency with the registered type and
argument count. This is the default for ‘R CMD check --as-cran’ or can
be enabled by setting environment variable ‘_R_CHECK_FF_CALLS_’ to
‘registration’ (but is in any case suppressed by ‘--install=no’).
Because this checks calls in which ‘.NAME’ is an R object and not just
a literal character string, some other problems are detected for such
calls.
Functions ‘suppressForeignCheck()’ and ‘dontCheck()’ have been added to allow package authors to suppress false positive reports.
‘R CMD check --as-cran’ warns about a false value of the ‘DESCRIPTION’
field ‘BuildVignettes’ for Open Source packages, and ignores it. (An
Open Source package needs to have complete sources for its vignettes
which should be usable on a suitably well-equipped system).
‘R CMD check --no-rebuild-vignettes’ is defunct:
‘R CMD check --no-build-vignettes’ has been preferred since R 3.0.0.
‘R CMD build --no-vignettes’ is defunct:
‘R CMD build --no-build-vignettes’ has been preferred since R 3.0.0.
‘R CMD Sweave’ and ‘R CMD Stangle’ now process both Sweave and
non-Sweave vignettes. The ‘tools::buildVignette()’ function has been
added to do the same tasks from within R.
The flags returned by ‘R CMD config --ldflags’ and (where installed)
‘pkg-config --libs libR’ are now those needed to link a front-end
against the (shared or static) R library.
‘Sweave.sty’ has a new option ‘[inconsolata]’.
‘R CMD check’ customizations such as ‘_R_CHECK_DEPENDS_ONLY_’ make
available packages only in ‘LinkingTo’ only for installation, and not
for loading/runtime tests.
‘tools::checkFF()’ reports on ‘.C’ and ‘.Fortran’ calls with ‘DUP =
FALSE’ if argument ‘check_DUP’ is true. This is selected by ‘R CMD
check’ by default.
‘R CMD check --use-gct’ can be tuned to garbage-collect less frequently
using ‘gctorture2()’ _via_ the setting of environment variable
‘_R_CHECK_GCT_N_’.
Where supported, ‘tools::texi2dvi()’ limits the number of passes tried
to 20.
(Windows only) A function ‘R_WaitEvent()’ has been added (with
declaration in header‘R.h’) to block execution until the next event is
received by R.
Remapping in the ‘Rmath.h’ header can be suppressed by defining
‘R_NO_REMAP_RMATH’.
The remapping of ‘rround()’ in header ‘Rmath.h’ has been removed: use
‘fround()’ instead.
‘ftrunc()’ in header ‘Rmath.h’ is now a wrapper for the C99 function
‘trunc()’, which might as well be used in C code: ‘ftrunc()’ is still
needed for portable C++ code.
The never-documented remapping of ‘prec()’ to ‘fprec()’ in header
‘Rmath.h’ has been removed.
The included LAPACK subset now contains ‘ZGESDD’ and ‘ZGELSD’.
The function ‘LENGTH()’ now checks that it is only applied to vector
arguments. However, in packages ‘length()’ should be used. (In R
itself ‘LENGTH()’ is a macro without the function overhead of
‘length()’.)
Calls to ‘SET_VECTOR_ELT()’ and ‘SET_STRING_ELT()’ are now checked for
indices which are in-range: several packages were writing one element
beyond the allocated length.
‘allocVector3’ has been added which allows custom allocators to be used
for individual vector allocations.
‘chol(pivot = TRUE, LINPACK = TRUE)’ is defunct.
Arguments ‘EISPACK’ for ‘eigen()’ and ‘LINPACK’ for ‘chol()’, ‘chol2inv()’, ‘solve()’ and ‘svd()’ are ignored: LAPACK is always used.
‘.find.package()’ and ‘.path.package()’ are defunct: only the versions
without the initial dot introduced in R 2.13.0 have ever been in the
API.
Partial matching when using the ‘$’ operator _on data frames_ now
throws a warning and may become defunct in the future. If partial
matching is intended, replace ‘foo$bar’ by ‘foo[["bar", exact =
FALSE]]’.
The long-deprecated use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’
files has been removed: such sections are now ignored (with a warning).
‘package.skeleton()’'s deprecated argument ‘namespace’ has been
removed.
Many methods are no longer exported by package ‘stats’. They are all
registered on their generic, which should be called rather than calling
a method directly.
Functions ‘readNEWS()’ and ‘checkNEWS()’ in package ‘tools’ are
defunct.
‘download.file(method = "lynx")’ is deprecated.
‘.C(DUP = FALSE)’ and ‘.Fortran(DUP = FALSE)’ are now deprecated, and
may be disabled in future versions of R. As their help has long said,
‘.Call()’ is much preferred.
‘R CMD check’ notes such usages (by default).
Calling ‘lm.wfit()’ with no non-zero weights gave an array-overrun in
the Fortran code and a not very sensible answer. It is now
special-cased with a simpler answer (no ‘qr’ component).
Error messages involving non-syntactic names (e.g. as produced by
‘`\r`’ when that object does not exist) now encode the control
characters. (Reported by Hadley Wickham.)
‘getGraphicsEvent()’ caused 100% usage of one CPU in Windows.
(PR#15500)
‘nls()’ with no ‘start’ argument may now work inside another function
(scoping issue).
‘pbeta()’ and similar work better for very large (billions) ‘ncp’.
Where time zones have changed abbreviations over the years, the
software tries to more consistently use the abbreviation appropriate to
the time or if that is unknown, the current abbreviation. On some
platforms where the C function ‘localtime’ changed the ‘tzname’
variables the reported abbreviation could have been that of the last
time converted.
‘all.equal(list(1), identity)’ now works.
Bug fix for pushing viewports in ‘grid’ (reported by JJ Allaire and
Kevin Ushey).
NOTE for anyone poking around within the graphics engine display list (despite the warnings not to) that this changes what is recorded by ‘grid’ on the graphics engine display list.
Extra checks have been added for unit resolution and conversion in
‘grid’, to catch instances of division-by-zero. This may introduce
error messages in existing code and/or produce a different result in
existing code (but only where a non-finite location or dimension may
now become zero).
Some bugs in TRE have been corrected by updating from the ‘git’
repository. This allows R to be installed on some platforms for which
this was a blocker (PR#15087 suggests Linux on ARM and HP-UX).
‘?’ applied to a call to an S4 generic failed in several cases.
(PR#15680)
The implicit S4 generics for primitives with ‘...’ in their argument
list were incorrect. (PR#15690)
Bug fixes to ‘methods::callGeneric()’. (PR#15691)
The bug fix to ‘aggregrate()’ in PR#15004 introduced a new bug in the
case of no grouping variables. (PR#15699)
In rare cases printing deeply nested lists overran a buffer by one byte
and on a few platforms segfaulted. (PR#15679)
The dendrogram method of ‘as.dendrogram()’ was hidden accidentally,
(PR#15703), and ‘order.dendrogram(d)’ gave too much for a leaf ‘d’.
(PR#15702)
R would try to kill processes on exit that have pids ever used by a
child process spawned by ‘mcparallel’ even though the current process
with that pid was not actually its child.
‘cophenetic()’ applied to a ‘"dendrogram"’ object sometimes incorrectly
returned a ‘"Labels"’ attribute with dimensions. (PR#15706)
‘printCoefmat()’ called from quite a few ‘print()’ methods now obeys
small ‘getOption("width")’ settings, line wrapping the ‘"signif.
codes"’ legend appropriately. (PR#15708)
‘type.convert()’ (and hence ‘read.table(as.is = TRUE)’) returns a
character vector or factor when representing a numeric input as a
double would lose accuracy. Similarly for complex inputs.
If a file contains numeric data with unrepresentable numbers of decimal places that are intended to be read as numeric, specify ‘colClasses’ in ‘read.table()’ to be ‘"numeric"’.
‘tools::Rdiff(useDiff = FALSE)’ is closer to the POSIX definition of
‘diff -b’ (as distinct from the description in the ‘man’ pages of most
systems).
New function ‘anyNA()’, a fast version of ‘any(is.na(.))’, _where
neither ‘is.na()’ nor ‘any()’ has a relevant method_, based on a
proposal by Tim Hesterberg. (Wish of PR#15239.)
‘arrayInd(*, useNames = TRUE)’ and, analogously, ‘which(*, arr.ind =
TRUE)’ now make use of ‘names(.dimnames)’ when available.
‘is.unsorted()’ now also works for ‘raw’ vectors.
The ‘"table"’ method for ‘as.data.frame()’ (also useful as
‘as.data.frame.table()’) now passes ‘sep’ and ‘base’ arguments to
‘provideDimnames()’.
‘uniroot()’ gets new optional arguments, notably ‘extendInt’, allowing
to auto-extend the search interval when needed. The return value has
an extra component, ‘init.it’.
‘switch(f, ...)’ now warns when ‘f’ is a factor, as this typically
happens accidentally where the useR meant to pass a character string,
but ‘f’ is treated as integer (as always documented).
The parser has been modified to use less memory.
The way the unary operators (‘+ - !’) handle attributes is now more
consistent. If there is no coercion, all attributes (including class)
are copied from the input to the result: otherwise only names, dims and
dimnames are.
‘colorRamp()’ and ‘colorRampPalette()’ now allow non-opaque colours and
a ramp in opacity via the new argument ‘alpha = TRUE’. (Suggested by
Alberto Krone-Martins, but optionally as there are existing uses which
expect only RGB values.)
‘grid.show.layout()’ and ‘grid.show.viewport()’ get an optional ‘vp.ex’
argument.
There is a new function ‘find_gs_cmd()’ in the ‘tools’ package to
locate a GhostScript executable. (This is an enhanced version of a
previously internal function there.)
‘object.size()’ gains a ‘format()’ method.
There is a new family, ‘"ArialMT"’, for the ‘pdf()’ and ‘postscript()’
devices. This will only be rendered correctly on viewers which have
access to Monotype TrueType fonts (which are sometimes requested by
journals).
The text and PDF news files, including ‘NEWS’ and ‘NEWS.2’, have been
moved to the ‘doc’ directory.
‘combn(x, simplify = TRUE)’ now gives a factor result for factor input
‘x’ (previously user error). (Related to PR#15442.)
Added ‘utils::fileSnapshot()’ and ‘utils::changedFiles()’ functions to
allow snapshots and comparison of directories of files.
‘make.names(names, unique=TRUE)’ now tries to preserve existing names.
(Suggestion of PR#15452.)
New functions ‘cospi(x)’, ‘sinpi(x)’, and ‘tanpi(x)’, for more accurate
computation of ‘cos(pi*x)’, etc, both in R and the C API. Using these
gains accuracy in some cases, e.g., inside ‘lgamma()’ or ‘besselI()’.
(Suggested by Morten Welinder in PR#15529.)
‘print.table(x, zero.print = ".")’ now also has an effect when ‘x’ is
not integer-valued.
There is more support to explore the system's idea of time-zone names.
‘Sys.timezone()’ tries to give the current system setting by name (and
succeeds at least on Linux, OS X, Solaris and Windows), and
‘OlsonNames()’ lists the names in the system's Olson database.
‘Sys.timezone(location = FALSE)’ gives the previous behaviour.
Platforms with a 64-bit ‘time_t’ type are allowed to handle conversions
between the ‘"POSIXct"’ and ‘"POSIXlt"’ classes for date-times outside
the 32-bit range (before 1902 or after 2037): the existing workarounds
are used on other platforms. (Note that time-zone information for
post-2037 is speculative at best, and the OS services are tested for
known errors and so not used on OS X.)
Currently ‘time_t’ is usually ‘long’ and hence 64-bit on Unix-alike 64-bit platforms: however it several cases the time-zone database is 32-bit. On R for Windows it is 64-bit (for both architectures as from this version).
The ‘"save.defaults"’ option can include a value for
‘compression_level’. (Wish of PR#15579.)
‘colSums()’ and friends now have support for arrays and data-frame
columns with 2^31 or more elements.
‘as.factor()’ is faster when ‘f’ is an unclassed integer vector (for
example, when called from ‘tapply()’).
‘fft()’ now works with longer inputs, from the 12 million previously
supported up to 2 billion. (PR#15593)
Complex ‘svd()’ now uses LAPACK subroutine ‘ZGESDD’, the complex
analogue of the routine used for the real case.
Sweave now outputs ‘.tex’ files in UTF-8 if the input encoding is
declared to be UTF-8, regardless of the local encoding. The UTF-8
encoding may now be declared using a LaTeX comment containing the
string ‘%\SweaveUTF8’ on a line by itself.
‘file.copy()’ gains a ‘copy.date’ argument.
Printing of date-times will make use of the time-zone abbreviation in
use at the time, if known. For example, for Paris pre-1940 this could
be ‘LMT’, ‘PMT’, ‘WET’ or ‘WEST’. To enable this, the ‘"POSIXlt"’
class has an optional component ‘"zone"’ recording the abbreviation for
each element.
For platforms which support it, there is also a component ‘"gmtoff"’ recording the offset from GMT where known.
(On Windows, by default on OS X and optionally elsewhere.) The system
C function ‘strftime’ has been replaced by a more comprehensive version
with closer conformance to the POSIX 2008 standard.
‘dnorm(x, log = FALSE)’ is more accurate (but somewhat slower) for |x|
> 5; as suggested in PR#15620.
Some versions of the ‘tiff()’ device have further compression options.
‘read.table()’, ‘readLines()’ and ‘scan()’ have a new argument to
influence the treatment of embedded nuls.
Avoid duplicating the right hand side values in complex assignments
when possible. This reduces copying of replacement values in
expressions such as ‘Z$a <- a0’ and ‘ans[[i]] <- tmp’: some package
code has relied on there being copies. (Based on suggestions from
Michael Lawrence.)
The ‘fast’ argument of ‘KalmanLike()’, ‘KalmanRun()’ and
‘KalmanForecast()’ has been replaced by ‘update’, which instead of
updating ‘mod’ in place, optionally returns the updated model in an
attribute ‘"mod"’ of the return value.
‘arima()’ and ‘makeARIMA()’ get a new optional argument ‘SSinit’,
allowing the choice of a different *s*tate *s*pace initialization which
has been observed to be more reliable close to non-stationarity: see
PR#14682.
‘warning()’ has a new argument ‘noBreaks.’, to simplify post-processing
of output with ‘options(warn = 1)’.
‘pushBack()’ gains an argument ‘encoding’, to support reading of UTF-8
characters using ‘scan()’, ‘read.table()’ and related functions in a
non-UTF-8 locale.
‘all.equal.list()’ gets a new argument ‘use.names’ which by default
labels differing components by names (if they match) rather than by
integer index. Saved R output in packages may need to be updated.
The methods for ‘all.equal()’ and ‘attr.all.equal()’ now have argument
‘check.attributes’ after ‘...’ so it cannot be partially nor
positionally matched (as it has been, unintentionally).
A side effect is that some previously undetected errors of passing empty arguments (no object between commas) to ‘all.equal()’ are detected and reported.
There are explicit checks that ‘check.attributes’ is logical, ‘tolerance’ is numeric and ‘scale’ is ‘NULL’ or numeric. This catches some unintended positional matching.
The message for ‘all.equal.numeric()’ reports a ‘"scaled difference"’ only for ‘scale != 1’.
‘all.equal()’ now has a ‘"POSIXt"’ method replacing the ‘"POSIXct"’
method.
The ‘"Date"’ and ‘"POSIXt"’ methods of ‘seq()’ allows ‘by = "quarter"’
for completeness (‘by = "3 months"’ always worked).
‘file.path()’ removes any trailing separator on Windows, where they are
invalid (although sometimes accepted). This is intended to enhance the
portability of code written by those using POSIX file systems (where a
trailing ‘/’ can be used to confine path matching to directories).
New function ‘agrepl()’ which like ‘grepl()’ returns a logical vector.
‘fifo()’ is now supported on Windows. (PR#15600)
‘sort.list(method = "radix")’ now allows negative integers (wish of
PR#15644).
Some functionality of ‘print.ts()’ is now available in
‘.preformat.ts()’ for more modularity.
‘mcparallel()’ gains an option ‘detach=TRUE’ which allows to execute
code independently of the current session. It is based on a new
‘estranged=TRUE’ argument to ‘mcfork()’ which forks child processes
such that they become independent of the parent process.
The ‘pdf()’ device omits entirely circles and text at extremely small
sizes, since some viewers were failing on such files.
More changes to reduce copying of objects (contributed by Michael Lawrence).