This blog is updated daily.
A general description is here.
There is the beginnings of support for the recently approved C++20 standard, specified analogously to C++14 and C++17. There is currently only limited support for this in compilers, with flags such as ‘-std=c++20’ and ‘-std=c++2a’. For the time being the ‘configure’ test is of accepting one of these flags and compiling C++17 code.
‘R_withCallingErrorHandler’ is now available for establishing a calling handler in C code for conditions inheriting from class ‘error’.
New ‘classes’ argument for ‘suppressWarnings()’ and ‘suppressMessages()’ to selectively suppress only warnings or messages that inherit from particular classes. Based on patch from Lionel Henry submitted with PR#17619.
New make target ‘distcheck’ checks
• R can be rebuilt from the tarball created by ‘make dist’,
• the build from the tarball passes ‘make check-all’,
• the build installs and uninstalls,
• the source files are properly cleaned by ‘make distclean’.
‘socketConnection(server = FALSE)’ now respects the connection timeout also on Linux.
New function ‘activeBindingFunction()’ retrieves the function of an active binding.
Packages need to be (re-)installed under this version (4.0.0) of R.
‘R_withCallingErrorHandler’ is now avaiable for establishing a calling handler in C code for conditions inheriting from class ‘error’.
New ‘classes’ argument for ‘suppressWarnings()’ and ‘suppressMessages()’ to selectively only suppress warnings or messages that inherit from particular classes. Based on patch from Lionel Henry submitted with PR#17619.
The handling of ‘${FOO-bar}’ and ‘${FOO:-bar}’ in ‘Renviron’ files now follows POSIX shells (at least on a Unix-alike), so the first treats empty environment variables as set and the second does not. Previously both ignored empty variables. There are several uses of the first form in ‘etc/Renviron’.
‘unlink()’ gains a new argument ‘expand’ to disable wildcard and tilde expansion. Elements of ‘x’ of value ‘"~"’ are now ignored.
New ‘globalCallingHandlers()’ function to establish global condition handlers. This allows registering default handlers for specific condition classes. Developed in collaboration with Lionel Henry.
New function ‘tryInvokeRestart()’ to invoke a specified restart if one is available and return without signaling an error if no such restart is found. Contributed by Lionel Henry in PR#17598.
‘Rprof()’ gains a new argument ‘filter.callframes’ to request that intervening call frames due to lazy evaluation or explicit ‘eval()’ calls be omitted from the recorded profile data. Contributed by Lionel Henry in PR#17595.
‘summaryRprof()’ now should work correctly for the ‘Rprof(*, memory.profiling=TRUE)’ case with small chunk size (and ‘"tseries"’ or similar) thanks to a patch proposal by Benjamin Tyner, in PR#15886.
‘xgettext()’ ignores strings passed to ‘ngettext()’, since the latter is handled by ‘xngettext()’. Thanks to Daniele Medri for the report and all the recent work he has done on the Italian translations.
‘str(x)’ now shows the length of ‘attributes’ in some cases for a data frame ‘x’.
‘Rprof()’ gains a new argument ‘filter.callframes’ to request that intervening call frames due to lazy evaluation or explicit ‘eval()’ calls be omitted from the recorded profile data. Contributed by Lionel Henry in PR#17595.
New function ‘tryInvokeRestart()’ to invoke a specified restart if one is available and return without signaling an error if no such restart is found. Contributed by Lionel Henry in PR#17598.
New make target ‘distcheck’ checks that: R can be rebuilt from the tarball created by ‘dist’; the tarball build passes ‘check-all’; the build installs and uninstalls ; and the source files are properly cleaned by ‘distclean’.
New ‘globalCallingHandlers()’ function to establish global condition handlers. This allows registering default handlers for specific condition classes. Developed in collaboration with Lionel Henry.
New ‘globalCallingHandlers()’ function to establish global condition handlers. This allows registering multiple handlers for any condition class. Developed colaboration with Lionel Henry.
The ‘plot()’ S3 generic function is now in package ‘base’ rather than package ‘graphics’, as it is reasonable to have methods that do not use the ‘graphics’ package. The generic is currently re-exported from the ‘graphics’ namespace to allow packages importing it from there to continue working, but this may change in future.
Packages which define S4 generics for ‘plot()’ should be re-installed and package code using such generics from other packages needs to ensure that they are imported rather than rely on their being looked for on the search path (as in a namespace, the base namespace has precedence over the search path).
This version of R is built against the PCRE2 library for Perl-like regular expressions, if available. (On non-Windows platforms PCRE1 can optionally be used if PCRE2 is not available at build time.) The version of PCRE in use can be obtained _via_ ‘extSoftVersion()’: PCRE1 (formerly known as ‘PCRE’) has versions <= 8, PCRE2 versions >= 10.
A server socket connection, a new connection type representing a listening server socket, is created via ‘serverSocket()’ and can accept multiple socket connections via ‘socketAccept()’.
New function ‘socketTimeout()’ changes the connection timeout of a socket connection.
‘R CMD check --as-cran’ now runs ‘\donttest’ examples (which are run by ‘example()’) instead of instructing the tester to do so. This can be temporarily circumvented during development by setting environment variable ‘_R_CHECK_DONTTEST_EXAMPLES_’ to a false value.
‘anova.glm()’ and ‘anova.glmlist()’ computed incorrect score (Rao) tests in no-intercept cases. (André Gillibert, PR#17734)
Several cases of integer overflow detected by the ‘undefined behaviour sanitizer’ of ‘clang’ 10 have been circumvented. One in ‘rhyper()’ may change the generated value for large input values.
Server socket connection, a new connection type representing a listening server socket, is created via ‘serverSocket()’ and can accept multiple socket connections via ‘socketAccept()’.
New function ‘socketTimeout()’ changes connection timeout of a socket connection.
The time needed to start a homogeneous ‘PSOCK’ cluster on ‘localhost’ with many nodes has been significantly reduced (package ‘parallel’).
R falls back to copying when junction creation fails during package checking (patch from Duncan Murdoch).
‘socketConnection(server = FALSE)’ now respects connection timeout also on Linux.
‘socketConnection(server = FALSE)’ no longer leaks a connection that is available right away without waiting (e.g. on ‘localhost’).
Socket connections are now robust against spurious readability and spurious availability of an incoming connection.
‘blocking = FALSE’ is now respected also on the server side of a socket connection, allowing non-blocking read operations.
Some invalid specifications of the day-of-the-year (_via_ ‘%j’, e.g. day 366 in 2017) or week plus day-of-the-week are now detected by ‘strptime()’. They now return ‘NA’ but give a warning as they may have given random results or corrupted memory in earlier versions of R.
‘RTerm’ now accepts enhanced/arrow keys also with ConPTY.
R can can now be started _via_ the launcher icon in a user documents directory whose path is not representable in the system encoding.
‘socketConnection(server = FALSE)’ now returns instantly also on Windows when connection failure is signalled.
Problems with UTF-16 surrogate pairs have been fixed in several functions, including ‘tolower()’ and ‘toupper()’ (PR#17645).
R now uses a ‘stringsAsFactors = FALSE’ default, and hence by default no longer converts strings to factors in calls to ‘data.frame()’ and ‘read.table()’.
A large number of packages relied on the previous behaviour and so have needed/will need updating.
For ‘head(x, n)’ and ‘tail()’ the default and other S3 methods notably for _vector_ ‘n’, e.g. to get a “corner” of a matrix, has been extended to ‘array’'s of higher dimension thanks to the patch proposal by Gabe Becker in PR#17652. Consequently, optional argument ‘addrownums’ is deprecated and replaced by the (more general) argument ‘keepnums’. An invalid second argument ‘n’ now leads to typically more easily readable error messages.
Where they are available, ‘writeBin()’ allows long vectors.
‘Sys.glob()’ now supports all characters from the Unicode Basic Multilingual Plane, no longer corrupting some (less commonly used) characters (PR#17638).
‘Rterm’ now correctly displays multi-byte-coded characters representable in the current native encoding (at least on Windows 10 they were sometimes omitted, PR#17632).
‘scan()’ issues with UTF-8 data when running in a DBCS locale have been resolved (PR#16520, PR#16584).
‘matrix’ objects now also inherit from class ‘"array"’, so e.g., ‘class(diag(1))’ is ‘c("matrix", "array")’. This invalidates code incorrectly assuming that ‘class(matrix_obj))’ has length one.
S3 methods for class ‘"array"’ are now dispatched for ‘matrix’ objects.
There is a new syntax for specifying _raw_ character constants similar to the one used in C++: ‘r"(...)"’ with ‘...’ any character sequence not containing the sequence ‘)"’. This makes it easier to write strings that contain backslashes or both single and double quotes. For more details see ‘?Quotes’.
Reference counting is now used instead of the ‘NAMED’ mechanism for determining when objects can be safely mutated in base C code. This reduces the need for copying in some cases and should allow further optimizations in the future. It should help make the internal code easier to maintain.
This change is expected to have almost no impact on packages using supported coding practices in their C/C++ code.
This version of R is built against the PCRE2 library for Perl-like regular expressions, if available. (On non-Windows platforms PCRE1 can optionally be used if PCRE2 is not available at build time.) The version of PCRE in use can be obtained via ‘extSoftVersion()’: PCRE1 (formerly known as ‘PCRE’) has versions <= 8, PCRE2 versions >= 10.
Making PCRE2 available when building R from source is strongly recommended (preferably version 10.30 or later) as PCRE1 is no longer developed: version 8.44 is ‘likely to be the final release’.
The internal traceback object produced when an error is signalled (‘.Traceback’), now contains the ‘call’s rather than the _‘deparse()’d_ calls, deferring the deparsing to the user-level functions ‘.traceback()’ and ‘traceback()’. This fulfils the wish of PR#17580, reported including two patch proposals by Brodie Gaslam.
For ‘head(x, n)’ and ‘tail()’ the default and other S3 methods notably for _vector_ ‘n’, e.g. to get a “corner” of a matrix, hace been extended to ‘array’'s of higher dimension thanks to the patch proposal by Gabe Becker in PR#17652. Consequently, optional argument ‘addrownums’ is deprecated and replaced by the (more general) arguemnt ‘keepnums’. An invalid second argument ‘n’ now leads to typically more easily readable error messages.
Printing ‘methods(..)’ now uses a new ‘format()’ method.
‘sort.list(x)’ now works for non-atomic objects ‘x’ and ‘method = "auto"’ (the default) or ‘"radix"’ in cases ‘order(x)’ works.
Where they are thavailable, ‘writeBin()’ allows long vectors.
‘wilcox.test()’ enhancements: In the (non-paired) two-sample case, ‘Inf’ values are treated as very large for robustness consistency. If exact computations are used, the result now has ‘"exact"’ in the ‘method’ element of its return value. New arguments ‘tol.root’ and ‘digits.rank’ where the latter may be used for stability to treat very close numbers as ties.
‘readBin()’ and ‘writeBin()’ now report an error for an invalid ‘endian’ value. The affected code needs to be fixed with care as the old undocumented behavior was to swap endian-ness in such cases.
‘sequence()’ is now an S3 generic with an internally implemented default method, and gains arguments to generate more complex sequences. Based on code from the ‘S4Vectors’ Bioconductor package and the advice of Hervé Pagès.
The default fill colour for ‘hist()’ and ‘boxplot()’ is now ‘col = "lightgray"’.
The default order of the levels on the y-axis for ‘spineplot()’ and ‘cdplot()’ has been reversed.
New function ‘R_user_dir()’ in package ‘tools’ suggests paths appropriate for storing R-related user-specific data, configuration and cache files.
The internal implementation of ‘grid’ units has changed, but the only visible effects at user-level should be
• a slightly different print format for some units (especially unit arithmetic),
• faster performance (for unit operations) and
• two new functions ‘unitType()’ and ‘unit.psum()’.
Based on code contributed by Thomas Lin Pedersen.
For consistency, ‘N <- NULL; N[[1]] <- val’ now turns ‘N’ into a ‘list’ also when ‘val)’ has length one. This enables ‘dimnames(r1)[[1]] <- "R1"’ for a 1-row matrix ‘r1’, fixing PR#17719 reported by Serguei Sokol.
‘deparse(..)’, ‘dump(..)’, and ‘dput(x, control = "all")’ now include control option ‘"digits17"’ which typically ensures 1:1 invertibility. New option ‘control = "exact"’ ensures numeric exact invertibility via ‘"hexDigits"’.
When loading data sets via ‘read.table()’, ‘data()’ now uses ‘LC_COLLATE=C’ to ensure locale-independent results for possible string-to-factor conversions.
‘Rterm’ gains a new option ‘--workspace’ to specify the workspace to be restored. This allows equals to be part of the name when opening _via_ Windows file associations (reported by Christian Asseburg).
Either PCRE2 or PCRE1 >= 8.32 (Nov 2012) is required: the deprecated provision for 8.20-8.31 has been removed.
‘Sys.glob()’ on Windows now supports all characters from the Unicode
Basic Multilingual Plane, no longer corrupting (less commonly used)
characters (PR#17638).
(Windows) ‘Rterm’ now correctly displays multi-byte-coded characters
representable in the current native encoding (at least on Windows 10
they were sometimes omitted, PR#17632).
‘scan()’ issues with UTF-8 data when running in a DBCS locale (on
Windows) have been resolved (PR#16520,PR#16584).
A rare C-level array overflow in ‘chull()’ has been worked around.
Some invalid specifications of the day-of-the-year (_via_ ‘%j’) are now detected by ‘strptime()’ and give an error.
‘postscript(.., title = *)’ now signals an error when the title string contains a character which would produce corrupt PostScript, thanks to PR#17607 by Daisuko Ogawa.
A better error message for ‘contour(*, levels = Inf)’.
‘dnorm’ had a problematic corner case with ‘sd == -Inf’ or negative ‘sd’ which was not flagged as an error in all cases. Thanks to Stephen D. Weigand for reporting and Wang Jiefei for analyzing this; similar change has been made in ‘dlnorm()’.
Operator ‘?’ now has lower precedence than ‘=’ to work as documented, so ‘=’ behaves like ‘<-’ in help expressions (PR#16710).
‘smoothEnds(x)’ now returns ‘integer’ type in _both_ cases when ‘x’ is ‘integer’, thanks to a report and proposal by Bill Dunlap PR#17693.
‘subset()’ had problems with 0-col dataframes (reported by Bill Dunlap, PR#17721).
R now uses reference counting instead of the ‘NAMED’ mechanism for
determining when objects can be safely mutated in base C code. This
reduces the need for copying in some cases and should allow further
optimizations in the future. It should also help make the internal
code easier to maintain. This change is expected to have minimal
impact on packages not using unsupported coding practices in their
C/C++ code.
R is now built against a PCRE2 library for Perl-like regular
expressions. (On non-Windows platforms PCRE1 can optionally be used if
PCRE2 is not available at build time.) The version of PCRE in use can
be obtained via ‘extSoftVersion()’: PCRE1 has versions < 10, PCRE2
versions >= 10.
PCRE2 reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used with PCRE2, and is reported as ‘FALSE’ when that is in use.
Making PCRE2 available when building R from source is strongly recommended (preferably version 10.30 or later) as PCRE1 is no longer developed (it only receives bug fixes and has outdated Unicode tables)
R now uses reference counting instead of the ‘NAMED’ mechanism for determining when objects can be safely mutated in base C code. This reduces the need for copying in some cases and should allow further optimizations in the future. It should also help make the internal code easier to maintain.
This change is expected to have almost no impact on packages using supported coding practices in their C/C++ code.
R is built against a PCRE2 library for Perl-like regular expressions, if available. (On non-Windows platforms PCRE1 can optionally be used if PCRE2 is not available at build time.) The version of PCRE in use can be obtained via ‘extSoftVersion()’: PCRE1 has versions < 10, PCRE2 versions >= 10.
Making PCRE2 available when building R from source is strongly recommended (preferably version 10.30 or later) as PCRE1 is no longer developed (it only receives bug fixes and has outdated Unicode tables)
PCRE2 reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used with PCRE2, and is reported as ‘FALSE’ when that is in use.
‘N <- NULL; N[[1]] <- val’ now turns ‘N’ into a ‘list’ also when
‘length(val) == 1’, for consistency. This enables ‘dimnames(r1)[[1]]
<- "R1"’ for a 1-row matrix ‘r1’, fixing PR#17719, reported by Serguei
Sokol.
‘deparse(..)’, ‘dump(..)’, and ‘dput(x, control="all")’ now include
using control option ‘"digits17"’ which typically ensures 1:1
invertibility. New option ‘control = "exact"’ ensures numeric exact
invertibility via ‘"hexDigits"’.
When loading data sets via ‘read.table()’, ‘data()’ now uses
‘LC_COLLATE=C’ to ensure locale independent results for possible
string-to-factor conversions.
‘matrix’ objects now also inherit from class ‘"array"’, so e.g., ‘class(diag(1))’ is ‘c("matrix", "array")’. This invalidates code incorrectly assuming that ‘length(class(obj)) == 1’.
S3 methods for class ‘"array"’ are now dispatched for ‘matrix’ objects.
R now uses a ‘stringsAsFactors = FALSE’ default, and hence by default no longer converts strings to factors in calls to ‘data.frame()’ and ‘read.table()’.
A large number of packages relied on the previous behaviour and so have needed/wlll need updating.
The ‘plot()’ S3 generic function is now in package ‘base’ rather than package ‘graphics’, as it is reasonable to have methods that do not use the ‘graphics’ package. The generic is currently re-exported from the ‘graphics’ namespace to allow packages importing it from there to continue working, but this may change in future.
Packages which define S4 generics for ‘plot()’ should be re-installed and package code using such generics from other packages needs to ensure that they are imported rather than rely on their being looked for on the search path (as in a namespace, the base namespace has priority over the search path).
‘news()’ has been enhanced to cover the news on R 3.x and 2.x.
‘N <- NULL; N[[1]] <- val’ now turns ‘N’ into a ‘list’ also when ‘length(val) == 1’, for consistency. This enables ‘dimnames(r1)[[1]] <- "R1"’ for a 1-row matrix ‘r1’, fixing PR#17719, reported by Serguei Sokol.
‘deparse(..)’, ‘dump(..)’, and ‘dput(x, control="all")’ now include using control option ‘"digits17"’ which typically ensures 1:1 invertibility. New option ‘control = "exact"’ ensures numeric exact invertibility via ‘"hexDigits"’.
When loading data sets via ‘read.table()’, ‘data()’ now uses ‘LC_COLLATE=C’ to ensure locale independent results for possible string-to-factor conversions.
The included LAPACK has been updated to version 3.9.0 (for the included
routines, just bug fixes).
Fixed a C level integer overflow in ‘rhyper()’; reported by Benjamin
Tyner in PR#17694.
Uses of ‘url(gzcon(.))’ needing to extend buffer size have failed (with
HTTP/2 servers), reported by Gábor Csárdi.
‘predict(loess(..), se=TRUE)’ now errors out (instead of seg.faulting
etc) for large sample sizes, thanks to a report and patch by Benjamin
Tyner in PR#17121.
‘tools:assertCondition(., "error")’ and hence ‘assertError()’ no longer
return errors twice (invisibly).
‘update(form, new)’ in the case of a long ‘new’ formula sometimes
wrongly eliminated the intercept from ‘form’, or (more rarely) added a
garbage term (or seg.faulted !); the fix happened by simplifying the
C-level logic of ‘terms.formula()’. Reported by Mathias Ambühl in
PR#16326.
The error message from ‘stopifnot(.., <error producing call>)’ again
contains the full ‘"stopifnot(.......)"’ call: Its attempted
suppression did not work consistently.
On Windows, ‘download.file(., , "wininet", headers=character())’ would
fail; reported with patch proposal by Kevin Ushey in PR#17710.
‘runmed(x, *)’ gains a new option ‘na.action’ determining _how_ to
handle ‘NaN’ or ‘NA’ in ‘x’.
‘dotchart()’ gains new options ‘ann’, ‘xaxt’, ‘frame.plot’ and ‘log’.
Detection of the C stack direction has been moved from run-time to
‘configure’: this is safer with LTO builds and allows the detection to
be overridden - see file ‘config.site’.
Source-code changes enable installation on platforms using ‘gcc
-fno-common’ (the expected default for ‘gcc 10.x’).
‘installTrChar’ (which is nowadays is wrapped by ‘installChar’) is
defined in ‘Rinternals.h’. (Neither are part of the API.)
Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at
installation which is used by the prototypes in headers ‘R_ext/BLAS.h’
and ‘R_ext/Lapack.h’ but to avoid extensive breakage this is only
exposed when ‘USE_FC_LEN_T’ is defined.
If a package's C/C++ calls to BLAS/LAPACK allow for the ‘hidden’ arguments used by most Fortran compilers to pass the lengths of Fortran character arguments, define ‘USE_FC_LEN_T’ and include ‘Rconfig.h’ (possibly _via_ ‘R.h’) before including ‘R_ext/BLAS.h’ or ‘R_ext/Lapack.h’.
A package with Fortran source code and perhaps C (but not C++) sources
can request for its shared object/DLL to be linked by the Fortran
compiler by including a line ‘USE_FC_TO_LINK=’ in ‘src/Makevars[.win]’
and using ‘$(SHLIB_OPENMP_FFLAGS)’ as part of ‘PKG_LIBS’.
The known reason for doing so is a package which uses Fortran (only) OpenMP on a platform where the Fortran OpenMP runtime is incompatible with the C one (e.g. ‘gfortran’ 9.x with ‘clang’).
‘R CMD check’ has a new option to mitigate checks leaving
files/directories in ‘/tmp’. See the ‘R Internals’ manual - this is
part of ‘--as-cran’.
The default standard for C++ in package installation is C++11 (as it
has been on other platforms where available since R 3.6.0: the default
toolchain on Windows was defaulting to C++98).
Support for specifying C++98 in package installation is deprecated.
Support in ‘R CMD config’ for ‘F77’, ‘FCPIFCPLAGS’, ‘CPP’, ‘CXXCPP’ and
‘CXX98’ and similar is deprecated. (‘CPP’ is found from the system
‘make’ and may well not be set.)
Use ‘$CC -E’ and ‘$CXX -E’ instead of ‘CPP’ and ‘CXXCPP’.
‘runmed(x, *)’ when ‘x’ contains missing values now works consistently
for both ‘algorithm="Stuetzle"’ and ‘"Turlach"’, and no longer
segfaults for ‘"Turlach"’, as reported by Hilmar Berger.
‘apply(diag(3), 2:3, mean)’ now gives a helpful error message.
‘dgamma(x, shape, log=TRUE)’ now longer overflows to ‘Inf’ for shape <
1 and very small ‘x’, fixing PR#17577, reported by Jonathan Rougier.
Buffer overflow in building error messages fixed. Reported by Benjamin
Tremblay.
‘options(str = .)’ is correctly initialized at package ‘utils’ load
time, now. A consequence is that ‘str()’ in scripts now is more
consistent to interactive use, e.g., when displaying function(**)
argument lists.
‘as.numeric(<call>)’ now gives correct error message.
Printing ‘ls.str()’ no longer wrongly shows ‘"<missing>"’ in rare
cases.
Auto-printing S4 objects no longer duplicates the object, for faster
speed and reduced memory consumption. Reported by Aaron Lun.
‘pchisq(<LRG>, <LRG>, ncp=100)’ no longer takes practically forever in
some cases. Hence ditto for corresponding ‘qchisq()’ calls.
‘x %% L’ for finite ‘x’ no longer returns ‘NaN’ when ‘L’ is infinite,
nor suffers from cancellation for large finite ‘L’, thanks to Long Qu's
PR#17611.
Analogously, ‘x %/% L’ and ‘L %/% x’ suffer less from cancellation and return values corresponding to limits for large ‘L’.
‘grepl(NA, *)’ now returns ‘logical’ as documented.
‘options(warn=1e11)’ is an error now, instead of later leading to C
stack overflow because of infinite recursion.
‘R_tryCatch’ no longer transfers control for all conditions. Reported
and patch provided by Lionel Henry in PR#17617.
‘format(object.size(.), digits=NULL)’ now works, fixing PR#17628
reported by Jonathan Carroll.
‘get_all_vars(f, d)’ now also works for cases, e.g. where ‘d’ contains
a matrix. Reported by Simon Wood in 2009 and patch provided by Ben
Bolker in PR#13624.
Additionally, it now also works when some variables are data frames, fixing PR#14905, reported by Patrick Breheny.
‘barplot()’ could get spacings wrong if there were exactly two bars
PR#15522. Patch by Michael Chirico.
‘power.t.test()’ works in more cases when returning values of n smaller
than 2.
‘dotchart(*, pch=., groups=.)’ now works better. Reported by Robert
and confirmed by Nic Rochette in PR#16953.
‘canCoerce(obj, cl)’ no longer assumes ‘length(class(obj)) == 1’.
‘plot.formula(*, subset = *)’ now also works in a boundary case
reported by Robert Schlicht (TU Dresden).
‘readBin()’ and ‘writeBin()’ of a ‘rawConnection()’ now also work in
large cases, thanks to a report and proposal by Taeke Harkema in
PR#17665.
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’.
‘R CMD config’ knows the values of ‘AR’ and ‘RANLIB’, often set for LTO
builds.
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’.)
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 ‘function’s 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 ‘NA’s (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.
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()’.
‘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 Gábor Csárdi.
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.arg’s.
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.
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.
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.
‘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.
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.
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.)
‘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 Nordström.
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 Gábor
Csárdi, 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).
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.
New macro ‘F_VISIBILITY’ as an alternative to ‘F77_VISIBILITY’. This
will become the preferred form in R 3.6.0.
‘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.
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).
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.
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.
‘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.
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).
‘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 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.
‘gc()’ gets new argument ‘full’.
‘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 ‘NA’s,
mostly thanks to a patch by Pavel Krivitsky in PR#17366. The
‘ar.yw.default()’'s AIC computations have become more efficient by
using ‘determinant()’.
New ‘warnErrList()’ utility (from package ‘nlme’, improved).
By default the (arbitrary) signs of the loadings from ‘princomp()’ are
chosen so the first element is non-negative.
If ‘--default-packages’ is not used, then ‘Rscript’ now checks the
environment variable ‘R_SCRIPT_DEFAULT_PACKAGES’. If this is set, then
it takes precedence over ‘R_DEFAULT_PACKAGES’. If default packages are
not specified on the command line or by one of these environment
variables, then ‘Rscript’ now uses the same default packages as ‘R’.
For now, the previous behavior of not including ‘methods’ can be
restored by setting the environment variable ‘R_SCRIPT_LEGACY’ to
‘yes’.
When a package is found more than once, the warning from
‘find.package(*, verbose=TRUE)’ lists all library locations.
POSIXt objects can now also be rounded or truncated to month or year.
‘stopifnot()’ can be used alternatively via new argument ‘exprs’ which
is nicer and useful when testing several expressions in one call.
The environment variable ‘R_MAX_VSIZE’ can now be used to specify the
maximal vector heap size. On macOS, unless specified by this
environment variable, the maximal vector heap size is set to the
maximum of 16GB and the available physical memory. This is to avoid
having the ‘R’ process killed when macOS over-commits memory.
‘sum(x)’ and ‘sum(x1, x2, .., x<N>)’ with many or long logical or
integer vectors no longer overflows (and returns ‘NA’ with a warning),
but returns ‘double’ numbers in such cases.
Single components of ‘"POSIXlt"’ objects can now be extracted and
replaced via ‘[’ indexing with 2 indices.
S3 method lookup now searches the namespace registry after the top
level environment of the calling environment.
Arithmetic sequences created by ‘1:n’, ‘seq_along’, and the like now
use compact internal representations via the ‘ALTREP’ framework.
Coercing integer and numeric vectors to character also now uses the
‘ALTREP’ framework to defer the actual conversion until first use.
Finalizers are now run with interrupts suspended.
‘merge()’ gains new option ‘no.dups’ and by default suffixes the second
of two duplicated column names, thanks to a proposal by Scott Ritchie
(and Gabe Becker).
‘scale.default(x, center, scale)’ now also allows ‘center’ or ‘scale’
to be “numeric-alike”, i.e., such that ‘as.numeric(.)’ coerces them
correctly. This also eliminates a wrong error message in such cases.
‘par*apply’ and ‘par*applyLB’ gain an optional argument ‘chunk.size’
which allows to specify the granularity of scheduling.
Some ‘as.data.frame()’ methods, notably the ‘matrix’ one, are now more
careful in not accepting duplicated or ‘NA’ row names, and by default
produce unique non-NA row names. This is based on new function
‘.rowNamesDF(x, make.names = *) <- rNms’ where the logical argument
‘make.names’ allows to specify _how_ invalid row names ‘rNms’ are
handled. ‘.rowNamesDF()’ is a “workaround” compatible default.
R has new serialization format (version 3) which supports custom
serialization of ‘ALTREP’ framework objects. These objects can still
be serialized in format 2, but less efficiently. Serialization format
3 also records the current native encoding of unflagged strings and
converts them when de-serialized in R running under different native
encoding. Format 3 comes with new serialization magic numbers (RDA3,
RDB3, RDX3). Format 3 can be selected by ‘version = 3’ in ‘save()’,
‘serialize()’ and ‘saveRDS()’, but format 2 remains the default for all
serialization and saving of the workspace. Serialized data in format 3
cannot be read by versions of R prior to version 3.5.0.
The ‘"Date"’ and “date-time” classes ‘"POSIXlt"’ and ‘"POSIXct"’ now
have a working ‘length<-()’ method, as wished in PR#17387.
‘optim(*, control = list(warn.1d.NelderMead = FALSE))’ allows to turn
off the warning when applying the default ‘"Nelder-Mead"’ method to
1-dimensional problems.
‘matplot(.., panel.first = .)’ etc now work, as ‘log’ becomes explicit
argument and ‘...’ is passed to ‘plot()’ unevaluated, as suggested by
Sebastian Meyer in PR#17386.
Interrupts can be suspended while evaluating an expression using
‘suspendInterrupts’. Subexpression can be evaluated with interrupts
enabled using ‘allowInterrupts’. These functions can be used to make
sure cleanup handlers cannot be interrupted.
R 3.5.0 includes a framework that allows packages to provide alternate
representations of basic R objects (‘ALTREP’). The framework is still
experimental and may undergo changes in future R releases as more
experience is gained. For now, documentation is provided in <URL:
https://svn.r-project.org/R/branches/ALTREP/ALTREP.html>.
‘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.
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).
‘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.
‘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.
‘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.)
‘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.
‘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.)
‘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.
‘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’.
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.
‘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.
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)
‘R CMD check’ checks for and ‘R CMD build’ corrects CRLF line endings
in shell scripts ‘configure’ and ‘cleanup’ (even on Windows).
The order of selection of OpenMP flags has been changed: Oracle
Developer Studio 12.5 accepts ‘-fopenmp’ and ‘-xopenmp’ but only the
latter enables OpenMP so it is now tried first.
‘within(List, rm(x1, x2))’ works correctly again, including when
‘List[["x2"]]’ is ‘NULL’.
‘regexec(pattern, text, *)’ now applies ‘as.character(.)’ to its first
two arguments, as documented.
‘write.table()’ and related functions, ‘writeLines()’, and perhaps
other functions writing text to connections did not signal errors when
the writes failed, e.g. due to a disk being full. Errors will now be
signalled if detected during the write, warnings if detected when the
connection is closed. (PR#17243)
‘rt()’ assumed the ‘ncp’ parameter was a scalar. (PR#17306)
‘menu(choices)’ with more than 10 choices which easily fit into one
‘getOption("width")’-line no longer erroneously repeats choices.
(PR#17312)
‘length()<-’ on a pairlist succeeds. (<URL:
https://stat.ethz.ch/pipermail/r-devel/2017-July/074680.html>)
Language objects such as ‘quote(("\n"))’ or R functions are correctly
printed again, where R 3.4.1 accidentally duplicated the backslashes.
Construction of ‘names()’ for very large objects in ‘c()’ and
‘unlist()’ now works, thanks to Suharto Anggono's patch proposals in
PR#17292.
Resource leaks (and similar) reported by Steve Grubb fixed. (PR#17314,
PR#17316, PR#17317, PR#17318, PR#17319, PR#17320)
‘model.matrix(~1, mf)’ now gets the row names from ‘mf’ also when they
differ from ‘1:nrow(mf)’, fixing PR#14992 thanks to the suggestion by
Sebastian Meyer.
‘sigma(fm)’ now takes the correct denominator degrees of freedom for a
fitted model with ‘NA’ coefficients. (PR#17313)
‘hist(x, "FD")’ no longer “dies” with a somewhat cryptic error message
when ‘x’ has extreme outliers or ‘IQR()’ zero: ‘nclass.FD(x)’ tries
harder to find a robust bin width h in the latter case, and
‘hist.default(*, breaks)’ now checks and corrects a too large ‘breaks’
number. (PR#17274)
‘callNextMethod()’ works for ‘...’ methods.
‘qr.coef(qd, y)’ now has correct names also when ‘qd’ is a complex QR
or stems from ‘qr(*, LAPACK=TRUE)’.
Setting ‘options(device = *)’ to an invalid function no longer
segfaults when plotting is initiated. (PR#15883)
‘encodeString(<very large string>)’ no longer segfaults. (PR#15885)
It is again possible to use ‘configure --enable-maintainer-mode’
without having installed ‘notangle’ (it was required in R 3.4.[01]).
S4 method dispatch on ‘...’ calls the method by name instead of
‘.Method’ (for consistency with default dispatch), and only attempts to
pass non-missing arguments from the generic.
‘readRDS(textConnection(.))’ works again. (PR#17325)
‘(1:n)[-n]’ no longer segfaults for ‘n <- 2.2e9’ (on a platform with
enough RAM).
‘x <- 1:2; tapply(x, list(x, x), function(x) "")[1,2]’ now correctly
returns ‘NA’. (PR#17333)
Running of finalizers after explicit GC request moved from the R
interface ‘do_gc’ to the ‘C’ interface ‘R_gc’. This helps with
reclaiming inaccessible connections.
‘help.search(topic)’ and ‘??topic’ matching topics in vignettes with
multiple file name extensions (e.g., ‘*.md.rsp’ but not ‘*.Rmd’) failed
with an error when using ‘options(help_type = "html")’.
The X11 device no longer uses the Xlib backing store (PR#16497).
‘array(character(), 1)’ now gives (a 1D array with) ‘NA’ as has been
documented for a long time as in the other cases of zero-length array
initialization and also compatibly with ‘matrix(character(), *)’. As
mentioned there, this also fixes PR#17333.
‘splineDesign(.., derivs = 4)’ no longer segfaults.
‘fisher.test(*, hybrid=TRUE)’ now (again) will use the hybrid method
when Cochran's conditions are met, fixing PR#16654.
The deprecated support for PCRE versions older than 8.20 has been
removed.
‘getParseData()’ gave incorrect column information when code contained
multi-byte characters. (PR#17254)
Asking for help using expressions like ‘?stats::cor()’ did not work.
(PR#17250)
‘readRDS(url(....))’ now works.
‘R CMD Sweave’ again returns ‘status = 0’ on successful completion.
Vignettes listed in ‘.Rbuildignore’ were not being ignored properly.
(PR#17246)
‘file.mtime()’ no longer returns NA on Windows when the file or
directory is being used by another process. This affected
‘installed.packages()’, which is now protected against this.
‘R CMD INSTALL’ Windows .zip file obeys ‘--lock’ and ‘--pkglock’ flags.
(Windows only) The ‘choose.files()’ function could return incorrect
results when called with ‘multi = FALSE’. (PR#17270)
‘aggregate(<data.frame>, drop = FALSE)’ now also works in case of
near-equal numbers in ‘by’. (PR#16918)
‘fourfoldplot()’ could encounter integer overflow when calculating the
odds ratio. (PR#17286)
‘parse()’ no longer gives spurious warnings when extracting srcrefs
from a file not encoded in the current locale.
This was seen from ‘R CMD check’ with ‘inst/doc/*.R’ files, and ‘check’ has some additional protection for such files.
‘print.noquote(x)’ now always returns its argument ‘x’ (invisibly).
Non-UTF-8 multibyte character sets were not handled properly in source
references. (PR#16732)
(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 ‘NA’s, also in its result no
longer setting them to ‘0’. Further, a new logical option ‘addNA’
allows to count ‘NA’s 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’.
User errors such as ‘integrate(f, 0:1, 2)’ are now caught.
Add ‘signature’ argument to ‘debug()’, ‘debugonce()’, ‘undebug()’ and
‘isdebugged()’ for more conveniently debugging S3 and S4 methods.
(Based on a patch by Gabe Becker.)
Add ‘utils::debugcall()’ and ‘utils::undebugcall()’ for debugging the
function that would be called by evaluating the given expression. When
the call is to an S4 generic or standard S3 generic, ‘debugcall()’
debugs the method that would be dispatched. A number of internal
utilities were added to support this, most notably
‘utils::isS3stdGeneric()’. (Based on a patch by Gabe Becker.)
Add ‘utils::strcapture()’. Given a character vector and a regular
expression containing capture expressions, ‘strcapture()’ will extract
the captured tokens into a tabular data structure, typically a
‘data.frame’.
‘str()’ and ‘strOptions()’ get a new option ‘drop.deparse.attr’ with
improved but _changed_ default behaviour for expressions. For
‘expression’ objects ‘x’, ‘str(x)’ now may remove extraneous white
space and truncate long lines.
‘str(<looooooooong_string>)’ is no longer very slow; inspired by Mikko
Korpela's proposal in PR#16527.
‘str(x)’'s default method is more “accurate” and hence somewhat more
generous in displaying character vectors; this will occasionally change
R outputs (and need changes to some ‘*.Rout(.save)’ files).
For a classed integer vector such as ‘x <- xtabs(~ c(1,9,9,9))’, ‘str(x)’ now shows both the class and ‘"int"’, instead of only the latter.
‘isSymmetric(m)’ is much faster for large asymmetric matrices ‘m’ _via_
pre-tests and a new option ‘tol1’ (with which strict back compatibility
is possible but not the default).
The result of ‘eigen()’ now is of class ‘"eigen"’ in the default case
when eigenvectors are computed.
Zero-length date and date-time objects (of classes ‘"POSIX[cl]?t"’) now
‘print()’ “recognizably”.
‘xy.coords()’ and ‘xyz.coords()’ get a new ‘setLab’ option.
The ‘method’ argument of ‘sort.list()’, ‘order()’ and ‘sort.int()’
gains an ‘"auto"’ option (the default) which should behave the same as
before when ‘method’ was not supplied.
‘stopifnot(E, ..)’ now reports differences when ‘E’ is a call to
‘all.equal()’ and that is not true.
‘boxplot(<formula>, *)’ gain optional arguments ‘drop’, ‘sep’, and
‘lex.order’ to pass to ‘split.default()’ which itself gains an argument
‘lex.order’ to pass to ‘interaction()’ for more flexibility.
The ‘plot()’ method for ‘ppr()’ has enhanced default labels (‘xmin’ and
‘main’).
‘sample.int()’ gains an explicit ‘useHash’ option (with a back
compatible default).
‘identical()’ gains an ‘ignore.srcref’ option which drops ‘"srcref"’
and similar attributes when true (as by default).
‘diag(x, nrow = n)’ now preserves ‘typeof(x)’, also for logical,
integer and raw ‘x’ (and as previously for complex and numeric).
‘smooth.spline()’ now allows direct specification of ‘lambda’, gets a
‘hatvalues()’ method and keeps ‘tol’ in the result, and optionally
parts of the internal matrix computations.
‘addNA()’ is faster now, e.g. when applied twice. (Part of PR#16895.)
New option ‘rstandard(<lm>, type = "predicted")’ provides the
“PRESS”-related leave-one-out cross-validation errors for linear
models.
After seven years of deprecation, duplicated factor levels now produce
a warning when printed and an error in ‘levels<-’ instead of a warning.
Invalid factors, e.g., with duplicated levels (invalid but
constructable) now give a warning when printed, _via_ new function
‘.valid.factor()’.
‘sessionInfo()’ has been updated for Apple's change in OS naming as
from ‘10.12’ (‘macOS Sierra’ _vs_ ‘OS X El Capitan’).
Its ‘toLatex()’ method now includes the ‘running’ component.
‘options(interrupt=)’ can be used to specify a default action for user
interrupts. For now, if this option is not set and the ‘error’ option
is set, then an unhandled user interrupt invokes the ‘error’ option.
(This may be dropped in the future as ‘interrupt’ conditions are not
‘error’ conditions.)
In most cases user interrupt handlers will be called with a ‘"resume"’
restart available. Handlers can invoke this restart to resume
computation. At the browser prompt the ‘r’ command will invoke a
‘"resume"’ restart if one is available. Some read operations cannot be
resumed properly when interrupted and do not provide a ‘"resume"’
restart.
Radix sort is now chosen by ‘method = "auto"’ for ‘sort.int()’ for
double vectors (and hence used for ‘sort()’ for unclassed double
vectors), excluding ‘long’ vectors.
‘sort.int(method = "radix")’ no longer rounds double vectors.
The ‘default’ and ‘data.frame’ methods for ‘stack()’ preserve the names
of empty elements in the levels of the ‘ind’ column of the return
value. Set the new ‘drop’ argument to ‘TRUE’ for the previous
behavior.
Speedup in ‘simplify2array()’ and hence ‘sapply()’ and ‘mapply()’ (for
the case of names and common length > 1), thanks to Suharto Anggono's
PR#17118.
‘table(x, exclude = NULL)’ now sets ‘useNA = "ifany"’ (instead of
‘"always"’). Together with the bug fixes for this case, this recovers
more consistent behaviour compatible to older versions of R. As a
consequence, ‘summary()’ for a logical vector no longer reports (zero)
counts for ‘NA’ when there are no ‘NA’s.
‘dump.frames()’ gets a new option ‘include.GlobalEnv’ which allows to
also dump the global environment, thanks to Andreas Kersting's proposal
in PR#17116.
‘system.time()’ now uses ‘message()’ instead of ‘cat()’ when terminated
early, such that ‘suppressMessages()’ has an effect; suggested by Ben
Bolker.
‘citation()’ supports ‘inst/CITATION’ files from package source trees,
with ‘lib.loc’ pointing to the directory containing the package.
‘try()’ gains a new argument ‘outFile’ with a default that can be
modified _via_ ‘options(try.outFile = .)’, useful notably for ‘Sweave’.
The unexported low-level functions in package ‘parallel’ for passing
serialized R objects to and from forked children now support long
vectors on 64-bit platforms. This removes some limits on higher-level
functions such as ‘mclapply()’ (but returning gigabyte results from
forked processes _via_ serialization should be avoided if at all
possible).
Connections now ‘print()’ without error even if invalid, e.g. after
having been destroyed.
‘apropos()’ and ‘find(simple.words = FALSE)’ no longer match object
names starting with ‘.’ which are known to be internal objects (such as
‘.__S3MethodsTable__.’).
Convenience function ‘hasName()’ has been added; it is intended to
replace the common idiom ‘!is.null(x$name)’ without the usually
unintended partial name matching.
‘strcapture()’ no longer fixes column names nor coerces strings to
factors (suggested by Bill Dunlap).
‘strcapture()’ returns ‘NA’ for non-matching values in ‘x’ (suggested
by Bill Dunlap).
‘source()’ gets new optional arguments, notably ‘exprs’; this is made
use of in the new utility function ‘withAutoprint()’.
‘sys.source()’ gets a new ‘toplevel.env’ argument. This argument is
useful for frameworks running package tests; contributed by Tomas
Kalibera.
‘Sys.setFileTime()’ and ‘file.copy(copy.date = TRUE)’ will set
timestamps with fractions of seconds on platforms/filesystems which
support this.
(Windows only.) ‘file.info()’ now returns file timestamps including
fractions of seconds; it has done so on other platforms since R 2.14.0.
(NB: some filesystems do not record modification and access timestamps
to sub-second resolution.)
The license check enabled by ‘options(checkPackageLicense = TRUE)’ is
now done when the package's namespace is first loaded.
‘ppr()’ and ‘supsmu()’ get an optional ‘trace’ argument, and ‘ppr(..,
sm.method = ..spline)’ is no longer limited to sample size n <= 2500.
The ‘POSIXct’ method for ‘print()’ gets optional ‘tz’ and ‘usetz’
arguments, thanks to a report from Jennifer S. Lyon.
New function ‘check_packages_in_dir_details()’ in package ‘tools’ for
analyzing package-check log files to obtain check details.
Package ‘tools’ now exports function ‘CRAN_package_db()’ for obtaining
information about current packages in the CRAN package repository, and
several functions for obtaining the check status of these packages.
The (default) Stangle driver ‘Rtangle’ allows ‘annotate’ to be a
function and gets a new ‘drop.evalFALSE’ option.
The default method for ‘quantile(x, prob)’ should now be monotone in
‘prob’, even in border cases, see PR#16672.
‘bug.report()’ now tries to extract an email address from a
‘BugReports’ field, and if there is none, from a ‘Contacts’ field.
The ‘format()’ and ‘print()’ methods for ‘object.size()’ results get
new options ‘standard’ and ‘digits’; notably, ‘standard = "IEC"’ and
‘standard = "SI"’ allow more standard (but less common) abbreviations
than the default ones, e.g. for kilobytes. (From contributions by
Henrik Bengtsson.)
If a reference class has a validity method, ‘validObject’ will be
called automatically from the default initialization method for
reference classes.
‘tapply()’ gets new option ‘default = NA’ allowing to change the
previously hardcoded value.
‘read.dcf()’ now consistently interprets any ‘whitespace’ to be
stripped to include newlines.
The maximum number of DLLs that can be loaded into R e.g. _via_
‘dyn.load()’ can now be increased by setting the environment variable
‘R_MAX_NUM_DLLS’ before starting R.
Assigning to an element of a vector beyond the current length now
over-allocates by a small fraction. The new vector is marked internally
as growable, and the true length of the new vector is stored in the
‘truelength’ field. This makes building up a vector result by assigning
to the next element beyond the current length more efficient, though
pre-allocating is still preferred. The implementation is subject to
change and not intended to be used in packages at this time.
Loading the ‘parallel’ package namespace no longer sets or changes the
‘.Random.seed’, even if ‘R_PARALLEL_PORT’ is unset.
NB: This can break reproducibility of output, and did for a CRAN package.
Methods ‘"wget"’ and ‘"curl"’ for ‘download.file()’ now give an R error
rather than a non-zero return value when the external command has a
non-zero status.
Encoding name ‘"utf8"’ is mapped to ‘"UTF-8"’. Many implementations of
‘iconv’ accept ‘"utf8"’, but not GNU ‘libiconv’ (including the late
2016 version 1.15).
‘sessionInfo()’ shows the full paths to the library or executable files
providing the BLAS/LAPACK implementations currently in use (not
available on Windows).
The binning algorithm used by bandwidth selectors ‘bw.ucv()’,
‘bw.bcv()’ and ‘bw.SJ()’ switches to a version linear in the input size
‘n’ for ‘n > nb/2’. (The calculations are the same, but for larger
‘n/nb’ it is worth doing the binning in advance.)
There is a new option ‘PCRE_study’ which controls when ‘grep(perl =
TRUE)’ and friends ‘study’ the compiled pattern. Previously this was
done for 11 or more input strings: it now defaults to 10 or more (but
most examples need many more for the difference from studying to be
noticeable).
‘grep(perl = TRUE)’ and friends can now make use of PCRE's Just-In-Time
mechanism, for PCRE >= 8.20 on platforms where JIT is supported. It is
used by default whenever the ‘pattern’ is studied (see the previous
item). (Based on a patch from Mikko Korpela.)
This is controlled by a new option ‘PCRE_use_JIT’.
Note that in general this makes little difference to the speed, and may take a little longer: its benefits are most evident on strings of thousands of characters. As a side effect it reduces the chances of C stack overflow in the PCRE library on very long strings (millions of characters, but see next item).
Warning: segfaults were seen using PCRE with JIT enabled on 64-bit Sparc builds.
There is a new option ‘PCRE_limit_recursion’ for ‘grep(perl = TRUE)’
and friends to set a recursion limit taking into account R's estimate
of the remaining C stack space (or 10000 if that is not available).
This reduces the chance of C stack overflow, but because it is
conservative may report a non-match (with a warning) in examples that
matched before. By default it is enabled if any input string has 1000
or more bytes. (PR#16757)
‘getGraphicsEvent()’ now works on ‘X11(type = "cairo")’ devices.
Thanks to Frederick Eaton (for reviving an earlier patch).
There is a new argument ‘onIdle’ for ‘getGraphicsEvent()’, which allows
an R function to be run whenever there are no pending graphics events.
This is currently only supported on X11 devices. Thanks to Frederick
Eaton.
The ‘deriv()’ and similar functions now can compute derivatives of
‘log1p()’, ‘sinpi()’ and similar one-argument functions, thanks to a
contribution by Jerry Lewis.
‘median()’ gains a formal ‘...’ argument, so methods with extra
arguments can be provided.
‘strwrap()’ reduces ‘indent’ if it is more than half ‘width’ rather
than giving an error. (Suggested by Bill Dunlap.)
When the condition ‘code’ in ‘if(.)’ or ‘while(.)’ is not of length
one, an error instead of a warning may be triggered by setting an
environment variable, see the help page.
Formatting and printing of bibliography entries (‘bibentry’) is more
flexible and better documented. Apart from setting
‘options(citation.bibtex.max = 99)’ you can also use ‘print(<citation>,
bibtex=TRUE)’ (or ‘format(..)’) to get the BibTeX entries in the case
of more than one entry. This also affects ‘citation()’. Contributions
to enable ‘style = "html+bibtex"’ are welcome.
Entry points ‘R_MakeExternalPtrFn’ and ‘R_ExternalPtrFn’ are now
declared in header ‘Rinternals.h’ to facilitate creating and retrieving
an R external pointer from a C function pointer without ISO C warnings
about the conversion of function pointers.
There was an exception for the native Solaris C++ compiler to the
dropping (in R 3.3.0) of legacy C++ headers from headers such as ‘R.h’
and ‘Rmath.h’ - this has now been removed. That compiler has strict
C++98 compliance hence does not include extensions in its (non-legacy)
C++ headers: some packages will need to request C++11 or replace
non-C++98 calls such as ‘lgamma’: see §1.6.4 of ‘Writing R Extensions’.
Because it is needed by about 70 CRAN packages, headers ‘R.h’ and ‘Rmath.h’ still declare
use namespace std;
when included on Solaris.
When included from C++, the R headers now use forms such as ‘std::FILE’
directly rather than including the line
using std::FILE;
C++ code including these headers might be relying on the latter.
Headers ‘R_ext/BLAS.h’ and ‘R_ext/Lapack.h’ have many improved
declarations including ‘const’ for double-precision complex routines.
_Inter alia_ this avoids warnings when passing ‘string literal’
arguments from C++11 code.
Headers for Unix-only facilities ‘R_ext/GetX11Image.h’,
‘R_ext/QuartzDevice.h’ and ‘R_ext/eventloop.h’ are no longer installed
on Windows.
No-longer-installed headers ‘GraphicsBase.h’, ‘RGraphics.h’,
‘Rmodules/RX11.h’ and ‘Rmodules/Rlapack.h’ which had a LGPL license no
longer do so.
‘HAVE_UINTPTR_T’ is now defined where appropriate by ‘Rconfig.h’ so
that it can be included before ‘Rinterface.h’ when ‘CSTACK_DEFNS’ is
defined and a C compiler (not C++) is in use. ‘Rinterface.h’ now
includes C header ‘stdint.h’ or C++11 header ‘cstdint’ where needed.
Package ‘tools’ has a new function
‘package_native_routine_registration_skeleton()’ to assist adding
native-symbol registration to a package. See its help and §5.4.1 of
‘Writing R Extensions’ for how to use it. (At the time it was added it
successfully automated adding registration to over 90% of CRAN packages
which lacked it. Many of the failures were newly-detected bugs in the
packages, e.g. 50 packages called entry points with varying numbers of
arguments and 65 packages called entry points not in the package.)
‘readline’ headers (and not just the library) are required unless
configuring with ‘--with-readline=no’.
‘configure’ now adds a compiler switch for C++11 code, even if the
compiler supports C++11 by default. (This ensures that ‘g++’ 6.x uses
C++11 mode and not its default mode of C++14 with ‘GNU extensions’.)
The tests for C++11 compliance are now much more comprehensive. For gcc < 4.8, the tests from R 3.3.0 are used in order to maintain the same behaviour on Linux distributions with long-term support.
An alternative compiler for C++11 is now specified with ‘CXX11’, not
‘CXX1X’. Likewise C++11 flags are specified with ‘CXX11FLAGS’ and the
standard (e.g., ‘-std=gnu++11’) is specified with ‘CXX11STD’.
‘configure’ now tests for a C++14-compliant compiler by testing some
basic features. This by default tries flags for the compiler specified
by ‘CXX11’, but an alternative compiler, options and standard can be
specified by variables ‘CXX14’, ‘CXX14FLAGS’ and ‘CXX14STD’ (e.g.,
‘-std=gnu++14’).
There is a new macro ‘CXXSTD’ to help specify the standard for C++
code, e.g. ‘-std=c++98’. This makes it easier to work with compilers
which default to a later standard: for example, with ‘CXX=g++6
CXXSTD=-std=c++98’ ‘configure’ will select commands for ‘g++’ 6.x which
conform to C++11 and C++14 where specified but otherwise use C++98.
Support for the defunct IRIX and OSF/1 OSes and Alpha CPU has been
removed.
‘configure’ checks that the compiler specified by ‘$CXX $CXXFLAGS’ is
able to compile C++ code.
‘configure’ checks for the required header ‘sys/select.h’ (or
‘sys/time.h’ on legacy systems) and system call ‘select’ and aborts if
they are not found.
If available, the POSIX 2008 system call ‘utimensat’ will be used by
‘Sys.setFileTime()’ and ‘file.copy(copy.date = TRUE)’. This may result
in slightly more accurate file times. (It is available on Linux and
FreeBSD but not macOS.)
The minimum version requirement for ‘libcurl’ has been reduced to
7.22.0, although at least 7.28.0 is preferred and earlier versions are
little tested. (This is to support Debian 7 ‘Wheezy’ LTS and Ubuntu
‘Precise’ 12.04 LTS, although the latter is close to end-of-life.)
‘configure’ tests for a C++17-compliant compiler. The tests are
experimental and subject to change in the future.
(Windows only) Tcl/Tk version 8.6.4 is now included in the binary
builds. The ‘tcltk*.chm’ help file is no longer included; please
consult the online help at <URL: http://www.tcl.tk/man/> instead.
The version of LAPACK included in the sources has been updated to
3.7.0: no new routines have been added to R.
There is support for compiling C++14 or C++17 code in packages on
suitable platforms: see ‘Writing R Extensions’ for how to request this.
The order of flags when ‘LinkingTo’ other packages has been changed so
their include directories come earlier, before those specified in
‘CPPFLAGS’. This will only have an effect if non-system include
directories are included with ‘-I’ flags in ‘CPPFLAGS’ (and so not the
default ‘-I/usr/local/include’ which is treated as a system include
directory on most platforms).
Packages which register native routines for ‘.C’ or ‘.Fortran’ need to
be re-installed for this version (unless installed with R-devel SVN
revision r72375 or later).
Make variables with names containing ‘CXX1X’ are deprecated in favour
of those using ‘CXX11’, but for the time being are still made available
_via_ file ‘etc/Makeconf’. Packages using them should be converted to
the new forms and made dependent on ‘R (>= 3.4.0)’.
Running ‘R CMD check --as-cran’ with ‘_R_CHECK_CRAN_INCOMING_REMOTE_’
false now skips tests that require remote access. The remaining
(local) tests typically run quickly compared to the remote tests.
‘R CMD build’ will now give priority to vignettes produced from files
in the ‘vignettes’ directory over those in the ‘inst/doc’ directory,
with a warning that the latter are being ignored.
‘R CMD config’ gains a ‘--all’ option for printing names and values of
all basic configure variables.
It now knows about all the variables used for the C++98, C++11 and C++14 standards.
‘R CMD check’ now checks that output files in ‘inst/doc’ are newer than
the source files in ‘vignettes’.
For consistency with other package subdirectories, files named ‘*.r’ in
the ‘tests’ directory are now recognized as tests by ‘R CMD check’.
(Wish of PR#17143.)
‘R CMD build’ and ‘R CMD check’ now use the _union_ of ‘R_LIBS’ and
‘.libPaths()’. They may not be equivalent, e.g., when the latter is
determined by ‘R_PROFILE’.
‘R CMD build’ now preserves dates when it copies files in preparing the
tarball. (Previously on Windows it changed the dates on all files; on
Unix, it changed some dates when installing vignettes.)
The new option ‘R CMD check --no-stop-on-test-error’ allows running the
remaining tests (under ‘tests/’) even if one gave an error.
Check customization _via_ environment variables to detect side effects
of ‘.Call()’ and ‘.External()’ calls which alter their arguments is
described in §8 of the ‘R Internals’ manual.
‘R CMD check’ now checks any ‘BugReports’ field to be non-empty and a
suitable single URL.
‘R CMD check --as-cran’ now NOTEs if the package does not register its
native routines or does not declare its intentions on (native) symbol
search. (This will become a WARNING in due course.)
(Windows only) Function ‘setInternet2()’ is defunct.
Installation support for ‘readline’ emulations based on ‘editline’ (aka
‘libedit’) is deprecated.
Use of the C/C++ macro ‘NO_C_HEADERS’ is defunct and silently ignored.
‘unix.time()’, a traditional synonym for ‘system.time()’, has been
deprecated.
‘structure(NULL, ..)’ is now deprecated as you cannot set attributes on
‘NULL’.
Header ‘Rconfig.h’ no longer defines ‘SUPPORT_OPENMP’; instead use
‘_OPENMP’ (as documented for a long time).
(C-level Native routine registration.) The deprecated ‘styles’ member
of the ‘R_CMethodDef’ and ‘R_FortranMethodDef’ structures has been
removed. Packages using these will need to be re-installed for R
3.4.0.
The deprecated support for PCRE versions older than 8.20 will be
removed in R 3.4.1. (Versions 8.20-8.31 will still be accepted but
remain deprecated.)
Getting or setting ‘body()’ or ‘formals()’ on non-functions for now
signals a warning and may become an error for setting.
‘match(x, t)’, ‘duplicated(x)’ and ‘unique(x)’ work as documented for
complex numbers with ‘NA’s or ‘NaN’s, where all those containing ‘NA’
do match, whereas in the case of ‘NaN’'s both real and imaginary parts
must match, compatibly with how ‘print()’ and ‘format()’ work for
complex numbers.
‘deparse(<complex>, options = "digits17")’ prints more nicely now,
mostly thanks to a suggestion by Richie Cotton.
Rotated symbols in plotmath expressions are now positioned correctly on
‘x11(type = "Xlib")’. (PR#16948)
‘as<-()’ avoids an infinite loop when a virtual class is interposed
between a subclass and an actual superclass.
Fix level propagation in ‘unlist()’ when the list contains zero-length
lists or factors.
Fix S3 dispatch on S4 objects when the ‘methods’ package is not
attached.
Internal S4 dispatch sets ‘.Generic’ in the method frame for
consistency with ‘standardGeneric()’. (PR#16929)
Fix ‘order(x, decreasing = TRUE)’ when ‘x’ is an integer vector
containing ‘MAX_INT’. Ported from a fix Matt Dowle made to
‘data.table’.
Fix caching by ‘callNextMethod()’, resolves PR#16973 and PR#16974.
‘grouping()’ puts NAs last, to be consistent with the default behavior
of ‘order()’.
Point mass limit cases: ‘qpois(-2, 0)’ now gives ‘NaN’ with a warning
and ‘qgeom(1, 1)’ is ‘0’. (PR#16972)
‘table()’ no longer drops an ‘"NaN"’ factor level, and better obeys
‘exclude = <chr>’, thanks to Suharto Anggono's patch for PR#16936.
Also, in the case of ‘exclude = NULL’ and ‘NA’s, these are tabulated
correctly (again).
Further, ‘table(1:2, exclude = 1, useNA = "ifany")’ no longer erroneously reports ‘<NA>’ counts.
Additionally, all cases of empty ‘exclude’ are equivalent, and ‘useNA’ is not overwritten when specified (as it was by ‘exclude = NULL’).
‘wilcox.test(x, conf.int=TRUE)’ no longer errors out in cases where the
confidence interval is not available, such as for ‘x = 0:2’.
‘droplevels(f)’ now keeps <NA> levels when present.
In integer arithmetic, ‘NULL’ is now treated as ‘integer(0)’ whereas it
was previously treated as ‘double(0)’.
The radix sort considers ‘NA_real_’ and ‘NaN’ to be equivalent in rank
(like the other sort algorithms).
When ‘index.return=TRUE’ is passed to ‘sort.int()’, the radix sort
treats ‘NA’s like ‘sort.list()’ does (like the other sort algorithms).
When in ‘tabulate(bin, nbin)’ ‘length(bin)’ is larger than the maximal
integer, the result is now of type ‘double’ and hence no longer
silently overflows to wrong values. (PR#17140)
‘as.character.factor()’ respects S4 inheritance when checking the type
of its argument. (PR#17141)
The ‘factor’ method for ‘print()’ no longer sets the class of the
factor to ‘NULL’, which would violate a basic constraint of an S4
object.
‘formatC(x, flag = f)’ allows two new flags, and signals an error for
invalid flags also in the case of character formatting.
Reading from ‘file("stdin")’ now also closes the connection and hence
no longer leaks memory when reading from a full pipe, thanks to Gábor
Csárdi, see thread starting at <URL:
https://stat.ethz.ch/pipermail/r-devel/2016-November/073360.html>.
Failure to create file in ‘tempdir()’ for compressed ‘pdf()’ graphics
device no longer errors (then later segfaults). There is now a warning
instead of error and compression is turned off for the device. Thanks
to Alec Wysoker (PR#17191).
Asking for ‘methods()’ on ‘"|"’ returns only S3 methods. See <URL:
https://stat.ethz.ch/pipermail/r-devel/2016-December/073476.html>.
‘dev.capture()’ using Quartz Cocoa device (macOS) returned invalid
components if the back-end chose to use ARGB instead of RGBA image
format. (Reported by Noam Ross.)
‘seq("2", "5")’ now works too, equivalently to ‘"2":"5"’ and
‘seq.int()’.
‘seq.int(to = 1, by = 1)’ is now correct, other cases are integer
(instead of ‘double’) when ‘seq()’ is integer too, and the "non-finite"
error messages are consistent between ‘seq.default()’ and ‘seq.int()’,
no longer mentioning ‘NaN’ etc.
‘rep(x, times)’ and ‘rep.int(x, times)’ now work when ‘times’ is larger
than the largest value representable in an integer vector. (PR#16932)
‘download.file(method = "libcurl")’ does not check for URL existence
before attempting downloads; this is more robust to servers that do not
support HEAD or range-based retrieval, but may create empty or
incomplete files for aborted download requests.
Bandwidth selectors ‘bw.ucv()’, ‘bw.bcv()’ and ‘bw.SJ()’ now avoid
integer overflow for large sample sizes.
‘str()’ no longer shows ‘"list output truncated"’, in cases that list
was not shown at all. Thanks to Neal Fultz (PR#17219)
Fix for ‘cairo_pdf()’ (and ‘svg()’ and ‘cairo_ps()’) when replaying a
saved display list that contains a mix of ‘grid’ and ‘graphics’ output.
(Report by Yihui Xie.)
The ‘str()’ and ‘as.hclust()’ methods for ‘"dendrogram"’ now also work
for deeply nested dendrograms thanks to non-recursive implementations
by Bradley Broom.
‘sample()’ now uses two uniforms for added precision when the uniform
generator is ‘Knuth-TAOCP’, ‘Knuth-TAOCP-2002’, or a user-defined
generator and the population size is 2^25 or greater.
If a vignette in the ‘vignettes’ directory is listed in
‘.Rbuildignore’, ‘R CMD build’ would not include it in the tarball, but
would include it in the vignette database, leading to a check warning.
(PR#17246)
‘tools::latexToUtf8()’ infinite looped on certain inputs. (PR#17138)
‘terms.formula()’ ignored argument names when determining whether two
terms were identical. (PR#17235)
‘callNextMethod()’ was broken when called from a method that augments
the formal arguments of a primitive generic.
Coercion of an S4 object to a vector during sub-assignment into a
vector failed to dispatch through the ‘as.vector()’ generic (often
leading to a segfault).
Fix problems in command completion: Crash (PR#17222) and junk display
in Windows, handling special characters in filenames on all systems.
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.
The ‘configure’ check for the ‘zlib’ version is now robust to versions
longer than 5 characters, including ‘1.2.11’.
Environmental variable ‘_R_CHECK_TESTS_NLINES_’ controls how ‘R CMD
check’ reports failing tests (see §8 of the ‘R Internals’ manual).
(C-level Native routine registration.) The undocumented ‘styles’ field
of the components of ‘R_CMethodDef’ and ‘R_FortranMethodDef’ is
deprecated.
‘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).
‘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.
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.
‘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).
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).
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 ‘0’s
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.)
‘R CMD INSTALL’ and hence ‘install.packages()’ gave an internal error
installing a package called ‘description’ from a tarball on a
case-insensitive file system.
‘match(x, t)’ (and hence ‘x %in% t’) failed when ‘x’ was of length one,
and either ‘character’ and ‘x’ and ‘t’ only differed in their
‘Encoding’ or when ‘x’ and ‘t’ where ‘complex’ with ‘NA’s or ‘NaN’s.
(PR#16885.)
‘unloadNamespace(ns)’ also works again when ‘ns’ is a ‘namespace’, as
from ‘getNamespace()’.
‘rgamma(1, Inf)’ or ‘rgamma(1, 0, 0)’ no longer give ‘NaN’ but the
correct limit.
‘length(baseenv())’ is correct now.
‘pretty(d, ..)’ for date-time ‘d’ rarely failed when ‘"halfmonth"’ time
steps were tried (PR#16923) and on ‘inaccurate’ platforms such as
32-bit Windows or a configuration with ‘--disable-long-double’; see
comment #15 of PR#16761.
In ‘text.default(x, y, labels)’, the rarely(?) used default for
‘labels’ is now correct also for the case of a 2-column matrix ‘x’ and
missing ‘y’.
‘as.factor(c(a = 1L))’ preserves ‘names()’ again as in R < 3.1.0.
‘strtrim(""[0], 0[0])’ now works.
Use of ‘Ctrl-C’ to terminate a reverse incremental search started by
‘Ctrl-R’ in the ‘readline’-based Unix terminal interface is now
supported when R was compiled against ‘readline’ >= 6.0 (‘Ctrl-G’
always worked). (PR#16603)
‘diff(<difftime>)’ now keeps the ‘"units"’ attribute, as subtraction
already did, PR#16940.
‘nchar(x, *)’'s argument ‘keepNA’ governing how the result for ‘NA’s in
‘x’ is determined, gets a new default ‘keepNA = NA’ which returns ‘NA’
where ‘x’ is ‘NA’, except for ‘type = "width"’ which still returns ‘2’,
the formatting / printing width of ‘NA’.
All builds have support for ‘https:’ URLs in the default methods for
‘download.file()’, ‘url()’ and code making use of them.
Unfortunately that cannot guarantee that any particular ‘https:’ URL can be accessed. For example, server and client have to successfully negotiate a cryptographic protocol (TLS/SSL, ...) and the server's identity has to be verifiable _via_ the available certificates. Different access methods may allow different protocols or use private certificate bundles: we encountered a ‘https:’ CRAN mirror which could be accessed by one browser but not by another nor by ‘download.file()’ on the same Linux machine.
The ‘print’ method for ‘methods()’ gains a ‘byclass’ argument.
New functions ‘validEnc()’ and ‘validUTF8()’ to give access to the
validity checks for inputs used by ‘grep()’ and friends.
Experimental new functionality for S3 method checking, notably
‘isS3method()’.
Also, the names of the R ‘language elements’ are exported as character vector ‘tools::langElts’.
‘str(x)’ now displays ‘"Time-Series"’ also for matrix (multivariate)
time-series, i.e. when ‘is.ts(x)’ is true.
(Windows only) The GUI menu item to install local packages now accepts
‘*.tar.gz’ files as well as ‘*.zip’ files (but defaults to the latter).
New programmeR's utility function ‘chkDots()’.
‘D()’ now signals an error when given invalid input, rather than
silently returning ‘NA’. (Request of John Nash.)
‘formula’ objects are slightly more “first class”: e.g., ‘formula()’ or
‘new("formula", y ~ x)’ are now valid. Similarly, for ‘"table"’,
‘"ordered"’ and ‘"summary.table"’. Packages defining S4 classes with
the above S3/S4 classes as slots should be reinstalled.
New function ‘strrep()’ for repeating the elements of a character
vector.
‘rapply()’ preserves attributes on the list when ‘how = "replace"’.
New S3 generic function ‘sigma()’ with methods for extracting the
estimated standard deviation aka “residual standard deviation” from a
fitted model.
‘news()’ now displays R and package news files within the HTML help
system if it is available. If no news file is found, a visible ‘NULL’
is returned to the console.
‘as.raster(x)’ now also accepts ‘raw’ arrays ‘x’ assuming values in
‘0:255’.
Subscripting of matrix/array objects of type ‘"expression"’ is now
supported.
‘type.convert("i")’ now returns a factor instead of a complex value
with zero real part and missing imaginary part.
Graphics devices ‘cairo_pdf()’ and ‘cairo_ps()’ now allow non-default
values of the cairographics ‘fallback resolution’ to be set.
This now defaults to 300 on all platforms: that is the default documented by cairographics, but apparently was not used by all system installations.
‘file()’ gains an explicit ‘method’ argument rather than implicitly
using ‘getOption("url.method", "default")’.
Thanks to a patch from Tomas Kalibera, ‘x[x != 0]’ is now typically
faster than ‘x[which(x != 0)]’ (in the case where ‘x’ has no NAs, the
two are equivalent).
‘read.table()’ now always uses the names for a named ‘colClasses’
argument (previously names were only used when ‘colClasses’ was too
short). (In part, wish of PR#16478.)
(Windows only) ‘download.file()’ with default ‘method = "auto"’ and a
‘ftps://’ URL chooses ‘"libcurl"’ if that is available.
The out-of-the box Bioconductor mirror has been changed to one using
‘https://’: use ‘chooseBioCmirror()’ to choose a ‘http://’ mirror if
required.
The data frame and formula methods for ‘aggregate()’ gain a ‘drop’
argument.
‘available.packages()’ gains a ‘repos’ argument.
The undocumented switching of methods for ‘url()’ on ‘https:’ and
‘ftps:’ URLs is confined to ‘method = "default"’ (and documented).
‘smoothScatter()’ gains a ‘ret.selection’ argument.
‘qr()’ no longer has a ‘...’ argument to pass additional arguments to
methods.
‘[’ has a method for class ‘"table"’.
It is now possible (again) to ‘replayPlot()’ a display list snapshot
that was created by ‘recordPlot()’ in a different R session.
It is still not a good idea to use snapshots as a persistent storage format for R plots, but it is now not completely silly to use a snapshot as a format for transferring an R plot between two R sessions.
The underlying changes mean that packages providing graphics devices (e.g., ‘Cairo’, ‘RSvgDevice’, ‘cairoDevice’, ‘tikzDevice’) will need to be reinstalled.
Code for restoring snapshots was contributed by Jeroen Ooms and JJ Allaire.
Some testing code is available at <URL: https://github.com/pmur002/R-display-list>.
‘tools::undoc(dir = D)’ and ‘codoc(dir = D)’ now also work when ‘D’ is
a directory whose ‘normalizePath()’ed version does not end in the
package name, e.g. from a symlink.
‘abbreviate()’ has more support for multi-byte character sets - it no
longer removes bytes within characters and knows about Latin vowels
with accents. It is still only really suitable for (most) European
languages, and still warns on non-ASCII input.
‘abbreviate(use.classes = FALSE)’ is now implemented, and that is more suitable for non-European languages.
‘match(x, table)’ is faster (sometimes by an order of magnitude) when
‘x’ is of length one and ‘incomparables’ is unchanged, thanks to Peter
Haverty (PR#16491).
More consistent, partly not back-compatible behavior of ‘NA’ and ‘NaN’
coercion to complex numbers, operations less often resulting in complex
‘NA’ (‘NA_complex_’).
‘lengths()’ considers methods for ‘length’ and ‘[[’ on ‘x’, so it
should work automatically on any objects for which appropriate methods
on those generics are defined.
The logic for selecting the default screen device on OS X has been
simplified: it is now ‘quartz()’ if that is available even if
environment variable ‘DISPLAY’ has been set by the user.
The choice can easily be overridden _via_ environment variable ‘R_INTERACTIVE_DEVICE’.
On Unix-like platforms which support the ‘getline’ C library function,
‘system(*, intern = TRUE)’ no longer truncates (output) lines longer
than 8192 characters, thanks to Karl Millar. (PR#16544)
‘rank()’ gains a ‘ties.method = "last"’ option, for convenience (and
symmetry).
‘regmatches(invert = NA)’ can now be used to extract both non-matched
and matched substrings.
‘data.frame()’ gains argument ‘fix.empty.names’; ‘as.data.frame.list()’
gets new ‘cut.names’, ‘col.names’ and ‘fix.empty.names’.
‘plot(x ~ x, *)’ now warns that it is the same as ‘plot(x ~ 1, *)’.
‘recordPlot()’ has new arguments ‘load’ and ‘attach’ to allow package
names to be stored as part of a recorded plot. ‘replayPlot()’ has new
argument ‘reloadPkgs’ to load/attach any package names that were stored
as part of a recorded plot.
S4 dispatch works within calls to ‘.Internal()’. This means explicit S4
generics are no longer needed for ‘unlist()’ and ‘as.vector()’.
Only font family names starting with ‘"Hershey"’ (and not ‘"Her"’ as
before) are given special treatment by the graphics engine.
S4 values are automatically coerced to vector (_via_ ‘as.vector’) when
subassigned into atomic vectors.
‘findInterval()’ gets a ‘left.open’ option.
The version of LAPACK included in the sources has been updated to
3.6.0, including those ‘deprecated’ routines which were previously
included. _Ca_ 40 double-complex routines have been added at the
request of a package maintainer.
As before, the details of what is included are in ‘src/modules/lapack/README’ and this now gives information on earlier additions.
‘tapply()’ has been made considerably more efficient without changing
functionality, thanks to proposals from Peter Haverty and Suharto
Anggono. (PR#16640)
‘match.arg(arg)’ (the one-argument case) is faster; so is ‘sort.int()’.
(PR#16640)
The ‘format’ method for ‘object_size’ objects now also accepts “binary”
units such as ‘"KiB"’ and e.g., ‘"Tb"’. (Partly from PR#16649.)
Profiling now records calls of the form ‘foo::bar’ and some similar
cases directly rather than as calls to ‘<Anonymous>’. Contributed by
Winston Chang.
New string utilities ‘startsWith(x, prefix)’ and ‘endsWith(x, suffix)’.
Also provide speedups for some ‘grepl("^...", *)’ uses (related to
proposals in PR#16490).
Reference class finalizers run at exit, as well as on garbage
collection.
Avoid ‘parallel’ dependency on ‘stats’ for port choice and random
number seeds. (PR#16668)
The radix sort algorithm and implementation from ‘data.table’
(‘forder’) replaces the previous radix (counting) sort and adds a new
method for ‘order()’. Contributed by Matt Dowle and Arun Srinivasan,
the new algorithm supports logical, integer (even with large values),
real, and character vectors. It outperforms all other methods, but
there are some caveats (see ‘?sort’).
The ‘order()’ function gains a ‘method’ argument for choosing between
‘"shell"’ and ‘"radix"’.
New function ‘grouping()’ returns a permutation that stably rearranges
data so that identical values are adjacent. The return value includes
extra partitioning information on the groups. The implementation came
included with the new radix sort.
‘rhyper(nn, m, n, k)’ no longer returns ‘NA’ when one of the three
parameters exceeds the maximal integer.
‘switch()’ now warns when no alternatives are provided.
‘parallel::detectCores()’ now has default ‘logical = TRUE’ on all
platforms - as this was the default on Windows, this change only
affects Sparc Solaris.
Option ‘logical = FALSE’ is now supported on Linux and recent versions of OS X (for the latter, thanks to a suggestion of Kyaw Sint).
‘hist()’ for ‘"Date"’ or ‘"POSIXt"’ objects would sometimes give
misleading labels on the breaks, as they were set to the day before the
start of the period being displayed. The display format has been
changed, and the shift of the start day has been made conditional on
‘right = TRUE’ (the default). (PR#16679)
R now uses a new version of the logo (donated to the R Foundation by
RStudio). It is defined in ‘.svg’ format, so will resize without
unnecessary degradation when displayed on HTML pages-there is also a
vector PDF version. Thanks to Dirk Eddelbuettel for producing the
corresponding X11 icon.
New function ‘.traceback()’ returns the stack trace which ‘traceback()’
prints.
‘lengths()’ dispatches internally.
‘dotchart()’ gains a ‘pt.cex’ argument to control the size of points
separately from the size of plot labels. Thanks to Michael Friendly
and Milan Bouchet-Valat for ideas and patches.
‘as.roman(ch)’ now correctly deals with more diverse character vectors
‘ch’; also arithmetic with the resulting roman numbers works in more
cases. (PR#16779)
‘prcomp()’ gains a new option ‘rank.’ allowing to directly aim for less
than ‘min(n,p)’ PC's. The ‘summary()’ and its ‘print()’ method have
been amended, notably for this case.
‘gzcon()’ gains a new option ‘text’, which marks the connection as
text-oriented (so e.g. ‘pushBack()’ works). It is still always opened
in binary mode.
The ‘import()’ namespace directive now accepts an argument ‘except’
which names symbols to exclude from the imports. The ‘except’
expression should evaluate to a character vector (after substituting
symbols for strings). See Writing R Extensions.
New convenience function ‘Rcmd()’ in package ‘tools’ for invoking ‘R
CMD’ tools from within R.
New functions ‘makevars_user()’ and ‘makevars_site()’ in package
‘tools’ to determine the location of the user and site specific
‘Makevars’ files for customizing package compilation.
‘R CMD check’ has a new option ‘--ignore-vignettes’ for use with
non-Sweave vignettes whose ‘VignetteBuilder’ package is not available.
‘R CMD check’ now by default checks code usage (_via_ ‘codetools’) with
only the base package attached. Functions from default packages other
than ‘base’ which are used in the package code but not imported are
reported as undefined globals, with a suggested addition to the
‘NAMESPACE’ file.
‘R CMD check --as-cran’ now also checks DOIs in package ‘CITATION’ and
Rd files.
‘R CMD Rdconv’ and ‘R CMD Rd2pdf’ each have a new option
‘--RdMacros=pkglist’ which allows Rd macros to be specified before
processing.
The previously included versions of ‘zlib’, ‘bzip2’, ‘xz’ and PCRE have
been removed, so suitable external (usually system) versions are
required (see the ‘R Installation and Administration’ manual).
The unexported and undocumented Windows-only devices ‘cairo_bmp()’,
‘cairo_png()’ and ‘cairo_tiff()’ have been removed. (These devices
should be used as e.g. ‘bmp(type = "cairo")’.)
(Windows only) Function ‘setInternet2()’ has no effect and will be
removed in due course. The choice between methods ‘"internal"’ and
‘"wininet"’ is now made by the ‘method’ arguments of ‘url()’ and
‘download.file()’ and their defaults can be set _via_ options. The
out-of-the-box default remains ‘"wininet"’ (as it has been since R
3.2.2).
‘[<-’ with an S4 value into a list currently embeds the S4 object into
its own list such that the end result is roughly equivalent to using
‘[[<-’. That behavior is deprecated. In the future, the S4 value will
be coerced to a list with ‘as.list()’.
Package ‘tools’' functions ‘package.dependencies()’, ‘pkgDepends()’,
etc are deprecated now, mostly in favor of ‘package_dependencies()’
which is both more flexible and efficient.
Support for very old versions of ‘valgrind’ (e.g., 3.3.0) has been
removed.
The included ‘libtool’ script (generated by ‘configure’) has been
updated to version 2.4.6 (from 2.2.6a).
‘libcurl’ version 7.28.0 or later with support for the ‘https’ protocol
is required for installation (except on Windows).
BSD networking is now required (except on Windows) and so
‘capabilities("http/ftp")’ is always true.
‘configure’ uses ‘pkg-config’ for PNG, TIFF and JPEG where this is
available. This should work better with multiple installs and with
those using static libraries.
The minimum supported version of OS X is 10.6 (‘Snow Leopard’): even
that has been unsupported by Apple since 2012.
The ‘configure’ default on OS X is ‘--disable-R-framework’: enable this
if you intend to install under ‘/Library/Frameworks’ and use with
‘R.app’.
The minimum preferred version of PCRE has since R 3.0.0 been 8.32
(released in Nov 2012). Versions 8.10 to 8.31 are now deprecated (with
warnings from ‘configure’), but will still be accepted until R 3.4.0.
‘configure’ looks for C functions ‘__cospi’, ‘__sinpi’ and ‘__tanpi’
and uses these if ‘cospi’ _etc_ are not found. (OS X is the main
instance.)
(Windows) R is now built using ‘gcc’ 4.9.3. This build will require
recompilation of at least those packages that include C++ code, and
possibly others. A build of R-devel using the older toolchain will be
temporarily available for comparison purposes.
During the transition, the environment variable ‘R_COMPILED_BY’ has been defined to indicate which toolchain was used to compile R (and hence, which should be used to compile code in packages). The ‘COMPILED_BY’ variable described below will be a permanent replacement for this.
(Windows) A ‘make’ and ‘R CMD config’ variable named ‘COMPILED_BY’ has
been added. This indicates which toolchain was used to compile R (and
hence, which should be used to compile code in packages).
The ‘make’ macro ‘AWK’ which used to be made available to files such as
‘src/Makefile’ is no longer set.
The API call ‘logspace_sum’ introduced in R 3.2.0 is now remapped as an
entry point to ‘Rf_logspace_sum’, and its first argument has gained a
‘const’ qualifier. (PR#16470)
Code using it will need to be reinstalled.
Similarly, entry point ‘log1pexp’ also defined in ‘Rmath.h’ is remapped there to ‘Rf_log1pexp’
‘R_GE_version’ has been increased to ‘11’.
New API call ‘R_orderVector1’, a faster one-argument version of
‘R_orderVector’.
When R headers such as ‘R.h’ and ‘Rmath.h’ are called from C++ code in
packages they include the C++ versions of system headers such as
‘<cmath>’ rather than the legacy headers such as ‘<math.h>’. (Headers
‘Rinternals.h’ and ‘Rinterface.h’ already did, and inclusion of system
headers can still be circumvented by defining ‘NO_C_HEADERS’, including
as from this version for those two headers.)
The manual has long said that R headers should *not* be included within an ‘extern "C"’ block, and almost all the packages affected by this change were doing so.
Including header ‘S.h’ from C++ code would fail on some platforms, and
so gives a compilation error on all.
The deprecated header ‘Rdefines.h’ is now compatible with defining
‘R_NO_REMAP’.
The connections interface now includes a function ‘R_GetConnection()’
which allows packages implementing connections to convert R
‘connection’ objects to ‘Rconnection’ handles. Code which previously
used the low-level R-internal ‘getConnection()’ entry point should
switch.
C-level ‘asChar(x)’ is fixed for when ‘x’ is not a vector, and it
returns ‘"TRUE"’/‘"FALSE"’ instead of ‘"T"’/‘"F"’ for logical vectors.
The first arguments of ‘.colSums()’ etc (with an initial dot) are now
named ‘x’ rather than ‘X’ (matching ‘colSums()’): thus error messages
are corrected.
A ‘coef()’ method for class ‘"maov"’ has been added to allow ‘vcov()’
to work with multivariate results. (PR#16380)
‘method = "libcurl"’ connections signal errors rather than retrieving
HTTP error pages (where the ISP reports the error).
‘xpdrows.data.frame()’ was not checking for unique row names; in
particular, this affected assignment to non-existing rows _via_
numerical indexing. (PR#16570)
‘tail.matrix()’ did not work for zero rows matrices, and could produce
row “labels” such as ‘"[1e+05,]"’.
Data frames with a column named ‘"stringsAsFactors"’ now format and
print correctly. (PR#16580)
‘cor()’ is now guaranteed to return a value with absolute value less
than or equal to 1. (PR#16638)
Array subsetting now keeps ‘names(dim(.))’.
Blocking socket connection selection recovers more gracefully on signal
interrupts.
The ‘data.frame’ method of ‘rbind()’ construction ‘row.names’ works
better in borderline integer cases, but may change the names assigned.
(PR#16666)
(X11 only) ‘getGraphicsEvent()’ miscoded buttons and missed mouse
motion events. (PR#16700)
‘methods(round)’ now also lists ‘round.POSIXt’.
‘tar()’ now works with the default ‘files = NULL’. (PR#16716)
Jumps to outer contexts, for example in error recovery, now make
intermediate jumps to contexts where ‘on.exit()’ actions are
established instead of trying to run all ‘on.exit()’ actions before
jumping to the final target. This unwinds the stack gradually, releases
resources held on the stack, and significantly reduces the chance of a
segfault when running out of C stack space. Error handlers established
using ‘withCallingHandlers()’ and ‘options("error")’ specifications are
ignored when handling a C stack overflow error as attempting one of
these would trigger a cascade of C stack overflow errors. (These
changes resolve PR#16753.)
The spacing could be wrong when printing a complex array. (Report and
patch by Lukas Stadler.)
‘pretty(d, n, min.n, *)’ for date-time objects ‘d’ works again in
border cases with large ‘min.n’, returns a ‘labels’ attribute also for
small-range dates and in such cases its returned length is closer to
the desired ‘n’. (PR#16761) Additionally, it finally does cover the
range of ‘d’, as it always claimed.
‘tsp(x) <- NULL’ did not handle correctly objects inheriting from both
‘"ts"’ and ‘"mts"’. (PR#16769)
‘install.packages()’ could give false errors when ‘options("pkgType")’
was ‘"binary"’. (Reported by Jose Claudio Faria.)
A bug fix in R 3.0.2 fixed problems with ‘locator()’ in X11, but
introduced problems in Windows. Now both should be fixed. (PR#15700)
‘download.file()’ with ‘method = "wininet"’ incorrectly warned of
download file length difference when reported length was unknown.
(PR#16805)
‘diag(NULL, 1)’ crashed because of missed type checking. (PR#16853)
‘format.POSIXlt()’ behaved incorrectly in R 3.2.4. E.g. the output of
‘format(as.POSIXlt(paste0(1940:2000, "-01-01"), tz = "CET"), usetz =
TRUE)’ ended in two ‘"CEST"’ time formats.
‘install.packages()’ and related functions now give a more informative
warning when an attempt is made to install a base package.
‘summary(x)’ now prints with less rounding when ‘x’ contains infinite
values. (Request of PR#16620.)
‘provideDimnames()’ gets an optional ‘unique’ argument.
‘shQuote()’ gains ‘type = "cmd2"’ for quoting in ‘cmd.exe’ in Windows.
(Response to PR#16636.)
The ‘data.frame’ method of ‘rbind()’ gains an optional argument
‘stringsAsFactors’ (instead of only depending on
‘getOption("stringsAsFactors")’).
‘smooth(x, *)’ now also works for long vectors.
‘tools::texi2dvi()’ has a workaround for problems with the ‘texi2dvi’
script supplied by ‘texinfo 6.1’.
It extracts more error messages from the LaTeX logs when in emulation mode.
‘R CMD check’ will leave a log file ‘build_vignettes.log’ from the
re-building of vignettes in the ‘.Rcheck’ directory if there is a
problem, and always if environment variable
‘_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_’ is set to a true value.
Use of ‘SUPPORT_OPENMP’ from header ‘Rconfig.h’ is deprecated in favour
of the standard OpenMP define ‘_OPENMP’.
(This has been the recommendation in the manual for a while now.)
The ‘make’ macro ‘AWK’ which is long unused by R itself but recorded in
file ‘etc/Makeconf’ is deprecated and will be removed in R 3.3.0.
The C header file ‘S.h’ is no longer documented: its use should be
replaced by ‘R.h’.
‘kmeans(x, centers = <1-row>)’ now works. (PR#16623)
‘Vectorize()’ now checks for clashes in argument names. (PR#16577)
‘file.copy(overwrite = FALSE)’ would signal a successful copy when none
had taken place. (PR#16576)
‘ngettext()’ now uses the same default domain as ‘gettext()’.
(PR#14605)
‘array(.., dimnames = *)’ now warns about non-‘list’ dimnames and, from
R 3.3.0, will signal the same error for invalid dimnames as ‘matrix()’
has always done.
‘addmargins()’ now adds dimnames for the extended margins in all cases,
as always documented.
‘heatmap()’ evaluated its ‘add.expr’ argument in the wrong environment.
(PR#16583)
‘require()’ etc now give the correct entry of ‘lib.loc’ in the warning
about an old version of a package masking a newer required one.
The internal deparser did not add parentheses when necessary, e.g.
before ‘[]’ or ‘[[]]’. (Reported by Lukas Stadler; additional fixes
included as well).
‘as.data.frame.vector(*, row.names=*)’ no longer produces ‘corrupted’
data frames from row names of incorrect length, but rather warns about
them. This will become an error.
‘url’ connections with ‘method = "libcurl"’ are destroyed properly.
(PR#16681)
‘withCallingHandler()’ now (again) handles warnings even during S4
generic's argument evaluation. (PR#16111)
‘deparse(..., control = "quoteExpressions")’ incorrectly quoted empty
expressions. (PR#16686)
‘format()’ting datetime objects (‘"POSIX[cl]?t"’) could segfault or
recycle wrongly. (PR#16685)
‘plot.ts(<matrix>, las = 1)’ now does use ‘las’.
‘saveRDS(*, compress = "gzip")’ now works as documented. (PR#16653)
(Windows only) The ‘Rgui’ front end did not always initialize the
console properly, and could cause R to crash. (PR#16698)
‘dummy.coef.lm()’ now works in more cases, thanks to a proposal by
Werner Stahel (PR#16665). In addition, it now works for multivariate
linear models (‘"mlm"’, ‘manova’) thanks to a proposal by Daniel
Wollschlaeger.
The ‘as.hclust()’ method for ‘"dendrogram"’s failed often when there
were ties in the heights.
‘reorder()’ and ‘midcache.dendrogram()’ now are non-recursive and hence
applicable to somewhat deeply nested dendrograms, thanks to a proposal
by Suharto Anggono in PR#16424.
‘cor.test()’ now calculates very small p values more accurately
(affecting the result only in extreme not statistically relevant
cases). (PR#16704)
‘smooth(*, do.ends=TRUE)’ did not always work correctly in R versions
between 3.0.0 and 3.2.3.
‘pretty(D)’ for date-time objects ‘D’ now also works well if ‘range(D)’
is (much) smaller than a second. In the case of only one unique value
in ‘D’, the pretty range now is more symmetric around that value than
previously.
Similarly, ‘pretty(dt)’ no longer returns a length 5 vector with duplicated entries for ‘Date’ objects ‘dt’ which span only a few days.
The figures in help pages such as ‘?points’ were accidentally damaged,
and did not appear in R 3.2.3. (PR#16708)
‘available.packages()’ sometimes deleted the wrong file when cleaning
up temporary files. (PR#16712)
The ‘X11()’ device sometimes froze on Red Hat Enterprise Linux 6. It
now waits for ‘MapNotify’ events instead of ‘Expose’ events, thanks to
Siteshwar Vashisht. (PR#16497)
‘[dpqr]nbinom(*, size=Inf, mu=.)’ now works as limit case, for ‘dpq’ as
the Poisson. (PR#16727)
‘pnbinom()’ no longer loops infinitely in border cases.
‘approxfun(*, method="constant")’ and hence ‘ecdf()’ which calls the
former now correctly “predict” ‘NaN’ values as ‘NaN’.
‘summary.data.frame()’ now displays ‘NA’s in ‘Date’ columns in all
cases. (PR#16709)
Some recently-added Windows time zone names have been added to the
conversion table used to convert these to Olson names. (Including
those relating to changes for Russia in Oct 2014, as in PR#16503.)
(Windows) Compatibility information has been added to the manifests for
‘Rgui.exe’, ‘Rterm.exe’ and ‘Rscript.exe’. This should allow
‘win.version()’ and ‘Sys.info()’ to report the actual Windows version
up to Windows 10.
Windows ‘"wininet"’ FTP first tries EPSV / PASV mode rather than only
using active mode (reported by Dan Tenenbaum).
‘which.min(x)’ and ‘which.max(x)’ may be much faster for logical and
integer ‘x’ and now also work for long vectors.
The ‘emulation’ part of ‘tools::texi2dvi()’ has been somewhat enhanced,
including supporting ‘quiet = TRUE’. It can be selected by ‘texi2dvi =
"emulation"’.
(Windows) MiKTeX removed its ‘texi2dvi.exe’ command in Sept 2015: ‘tools::texi2dvi()’ tries ‘texify.exe’ if it is not found.
(Windows only) Shortcuts for printing and saving have been added to
menus in ‘Rgui.exe’. (Request of PR#16572.)
‘loess(..., iterTrace=TRUE)’ now provides diagnostics for robustness
iterations, and the ‘print()’ method for ‘summary(<loess>)’ shows
slightly more.
The included version of PCRE has been updated to 8.38, a bug-fix
release.
‘View()’ now displays nested data frames in a more friendly way.
(Request with patch in PR#15915.)
The included configuration code for ‘libintl’ has been updated to that
from ‘gettext’ version 0.19.5.1 - this should only affect how an
external library is detected (and the only known instance is under
OpenBSD). (Wish of PR#16464.)
‘configure’ has a new argument ‘--disable-java’ to disable the checks
for Java.
The ‘configure’ default for ‘MAIN_LDFLAGS’ has been changed for the
FreeBSD, NetBSD and Hurd OSes to one more likely to work with compilers
other than ‘gcc’ (FreeBSD 10 defaults to ‘clang’).
‘configure’ now supports the OpenMP flags ‘-fopenmp=libomp’ (clang) and
‘-qopenmp’ (Intel C).
Various macros can be set to override the default behaviour of
‘configure’ when detecting OpenMP: see file ‘config.site’.
Source installation on Windows has been modified to allow for MiKTeX
installations without ‘texi2dvi.exe’. See file ‘MkRules.dist’.
‘regexpr(pat, x, perl = TRUE)’ with Python-style named capture did not
work correctly when ‘x’ contained ‘NA’ strings. (PR#16484)
The description of dataset ‘ToothGrowth’ has been improved/corrected.
(PR#15953)
‘model.tables(type = "means")’ and hence ‘TukeyHSD()’ now support
‘"aov"’ fits without an intercept term. (PR#16437)
‘close()’ now reports the status of a ‘pipe()’ connection opened with
an explicit ‘open’ argument. (PR#16481)
Coercing a list without names to a data frame is faster if the elements
are very long. (PR#16467)
(Unix-only) Under some rare circumstances piping the output from
‘Rscript’ or ‘R -f’ could result in attempting to close the input file
twice, possibly crashing the process. (PR#16500)
(Windows) ‘Sys.info()’ was out of step with ‘win.version()’ and did not
report Windows 8.
‘topenv(baseenv())’ returns ‘baseenv()’ again as in R 3.1.0 and
earlier. This also fixes ‘compilerJIT(3)’ when used in ‘.Rprofile’.
‘detach()’ing the ‘methods’ package keeps ‘.isMethodsDispatchOn()’
true, as long as the methods namespace is not unloaded.
Removed some spurious warnings from ‘configure’ about the preprocessor
not finding header files. (PR#15989)
‘rchisq(*, df=0, ncp=0)’ now returns ‘0’ instead of ‘NaN’, and
‘dchisq(*, df=0, ncp=*)’ also no longer returns ‘NaN’ in limit cases
(where the limit is unique). (PR#16521)
‘pchisq(*, df=0, ncp > 0, log.p=TRUE)’ no longer underflows (for ncp >
~60).
‘nchar(x, "w")’ returned -1 for characters it did not know about (e.g.
zero-width spaces): it now assumes 1. It now knows about most
zero-width characters and a few more double-width characters.
Help for ‘which.min()’ is now more precise about behavior with logical
arguments. (PR#16532)
The print width of character strings marked as ‘"latin1"’ or ‘"bytes"’
was in some cases computed incorrectly.
‘abbreviate()’ did not give names to the return value if ‘minlength’
was zero, unlike when it was positive.
(Windows only) ‘dir.create()’ did not always warn when it failed to
create a directory. (PR#16537)
When operating in a non-UTF-8 multibyte locale (e.g. an East Asian
locale on Windows), ‘grep()’ and related functions did not handle UTF-8
strings properly. (PR#16264)
‘read.dcf()’ sometimes misread lines longer than 8191 characters.
(Reported by Hervé Pagès with a patch.)
‘within(df, ..)’ no longer drops columns whose name start with a ‘"."’.
The built-in ‘HTTP’ server converted entire ‘Content-Type’ to lowercase
including parameters which can cause issues for multi-part form
boundaries (PR#16541).
Modifying slots of S4 objects could fail when the ‘methods’ package was
not attached. (PR#16545)
‘splineDesign(*, outer.ok=TRUE)’ (‘splines’) is better now (PR#16549),
and ‘interpSpline()’ now allows ‘sparse=TRUE’ for speedup with
non-small sizes.
If the expression in the traceback was too long, ‘traceback()’ did not
report the source line number. (Patch by Kirill Müller.)
The browser did not truncate the display of the function when exiting
with ‘options("deparse.max.lines")’ set. (PR#16581)
When ‘bs(*, Boundary.knots=)’ had boundary knots inside the data range,
extrapolation was somewhat off. (Patch by Trevor Hastie.)
‘var()’ and hence ‘sd()’ warn about ‘factor’ arguments which are
deprecated now. (PR#16564)
‘loess(*, weights = *)’ stored wrong weights and hence gave slightly
wrong predictions for ‘newdata’. (PR#16587)
‘aperm(a, *)’ now preserves ‘names(dim(a))’.
‘poly(x, ..)’ now works when either ‘raw=TRUE’ or ‘coef’ is specified.
(PR#16597)
‘data(package=*)’ is more careful in determining the path.
‘prettyNum(*, decimal.mark, big.mark)’: fixed bug introduced when
fixing PR#16411.
It is now easier to use secure downloads from ‘https://’ URLs on builds
which support them: no longer do non-default options need to be
selected to do so. In particular, packages can be installed from
repositories which offer ‘https://’ URLs, and those listed by
‘setRepositories()’ now do so (for some of their mirrors).
Support for ‘https://’ URLs is available on Windows, and on other platforms if support for ‘libcurl’ was compiled in and if that supports the ‘https’ protocol (system installations can be expected to do). So ‘https://’ support can be expected except on rather old OSes (an example being OS X ‘Snow Leopard’, where a non-system version of ‘libcurl’ can be used).
(Windows only) The default method for accessing URLs _via_ ‘download.file()’ and ‘url()’ has been changed to be ‘"wininet"’ using Windows API calls. This changes the way proxies need to be set and security settings made: there have been some reports of ‘ftp:’ sites being inaccessible under the new default method (but the previous methods remain available).
‘cmdscale()’ gets new option ‘list.’ for increased flexibility when a
list should be returned.
‘configure’ now supports ‘texinfo’ version 6.0, which (unlike the
change from 4.x to 5.0) is a minor update. (Wish of PR#16456.)
(Non-Windows only) ‘download.file()’ with default ‘method = "auto"’ now
chooses ‘"libcurl"’ if that is available and a ‘https://’ or ‘ftps://’
URL is used.
(Windows only) ‘setInternet2(TRUE)’ is now the default. The
command-line option ‘--internet2’ and environment variable
‘R_WIN_INTERNET2’ are now ignored.
Thus by default the ‘"internal"’ method for ‘download.file()’ and ‘url()’ uses the ‘"wininet"’ method: to revert to the previous default use ‘setInternet2(FALSE)’.
This means that ‘https://’ URLs can be read by default by ‘download.file()’ (they have been readable by ‘file()’ and ‘url()’ since R 3.2.0).
There are implications for how proxies need to be set (see ‘?download.file’).
‘chooseCRANmirror()’ and ‘chooseBioCmirror()’ now offer HTTPS mirrors
in preference to HTTP mirrors. This changes the interpretation of
their ‘ind’ arguments: see their help pages.
‘capture.output()’ gets optional arguments ‘type’ and ‘split’ to pass
to ‘sink()’, and hence can be used to capture messages.
Header ‘Rconfig.h’ now defines ‘HAVE_ALLOCA_H’ if the platform has the
‘alloca.h’ header (it is needed to define ‘alloca’ on Solaris and AIX,
at least: see ‘Writing R Extensions’ for how to use it).
The ‘libtool’ script generated by ‘configure’ has been modified to
support FreeBSD >= 10 (PR#16410).
The HTML help page links to demo code failed due to a change in R
3.2.0. (PR#16432)
If the ‘na.action’ argument was used in ‘model.frame()’, the original
data could be modified. (PR#16436)
‘getGraphicsEvent()’ could cause a crash if a graphics window was
closed while it was in use. (PR#16438)
‘matrix(x, nr, nc, byrow = TRUE)’ failed if ‘x’ was an object of type
‘"expression"’.
‘strptime()’ could overflow the allocated storage on the C stack when
the timezone had a non-standard format much longer than the standard
formats. (Part of PR#16328.)
‘options(OutDec = s)’ now signals a warning (which will become an error
in the future) when ‘s’ is not a string with exactly one character, as
that has been a documented requirement.
‘prettyNum()’ gains a new option ‘input.d.mark’ which together with
other changes, e.g., the default for ‘decimal.mark’, fixes some
‘format()’ting variants with non-default ‘getOption("OutDec")’ such as
in PR#16411.
‘download.packages()’ failed for ‘type’ equal to either ‘"both"’ or
‘"binary"’. (Reported by Dan Tenenbaum.)
The ‘dendrogram’ method of ‘labels()’ is much more efficient for large
dendrograms, now using ‘rapply()’. (Comment #15 of PR#15215)
The ‘"port"’ algorithm of ‘nls()’ could give spurious errors.
(Reported by Radford Neal.)
Reference classes that inherited from reference classes in another
package could invalidate methods of the inherited class. Fixing this
requires adding the ability for methods to be “external”, with the
object supplied explicitly as the first argument, named ‘.self’. See
"Inter-Package Superclasses" in the documentation.
‘readBin()’ could fail on the SPARC architecture due to alignment
issues. (Reported by Radford Neal.)
‘qt(*, df=Inf, ncp=.)’ now uses the natural ‘qnorm()’ limit instead of
returning ‘NaN’. (PR#16475)
Auto-printing of S3 and S4 values now searches for ‘print()’ in the
base namespace and ‘show()’ in the ‘methods’ namespace instead of
searching the global environment.
‘polym()’ gains a ‘coefs = NULL’ argument and returns class ‘"poly"’
just like ‘poly()’ which gets a new ‘simple=FALSE’ option. They now
lead to correct ‘predict()’ions, e.g., on subsets of the original data.
(PR#16239)
‘rhyper(nn, <large>)’ now works correctly. (PR#16489)
‘ttkimage()’ did not (and could not) work so was removed. Ditto for
‘tkimage.cget()’ and ‘tkimage.configure()’. Added two Ttk widgets and
missing subcommands for Tk's ‘image’ command: ‘ttkscale()’,
‘ttkspinbox()’, ‘tkimage.delete()’, ‘tkimage.height()’,
‘tkimage.inuse()’, ‘tkimage.type()’, ‘tkimage.types()’,
‘tkimage.width()’. (PR#15372, PR#16450)
‘getClass("foo")’ now also returns a class definition when it is found
in the cache more than once.
‘utf8ToInt()’ now checks that its input is valid UTF-8 and returns ‘NA’
if it is not.
‘install.packages()’ now allows ‘type = "both"’ with ‘repos = NULL’ if
it can infer the type of file.
‘nchar(x, *)’ and ‘nzchar(x)’ gain a new argument ‘keepNA’ which
governs how the result for ‘NA’s in ‘x’ is determined. For ‘nzchar()’
in general and ‘nchar()’ in the R 3.2.x series, the default remains
‘FALSE’ which is fully back compatible. From R 3.3.0, ‘nchar()’'s
default will change to ‘keepNA = NA’ and you are advised to consider
this for code portability.
‘news()’ more flexibly extracts dates from package ‘NEWS.Rd’ files.
‘lengths(x)’ now also works (trivially) for atomic ‘x’ and hence can be
used more generally as an efficient replacement of ‘sapply(x, length)’
and similar.
The included version of PCRE has been updated to 8.37, a bug-fix
release.
‘diag()’ no longer duplicates a matrix when extracting its diagonal.
‘as.character.srcref()’ gains an argument to allow characters
corresponding to a range of source references to be extracted.
‘acf()’ and ‘ccf()’ now guarantee values strictly in [-1,1] (instead of
sometimes very slightly outside). PR#15832.
‘as.integer("111111111111")’ now gives NA (with a warning) as it does
for the corresponding numeric or negative number coercions. Further,
‘as.integer(M + 0.1)’ now gives ‘M’ (instead of NA) when M is the
maximal representable integer.
On some platforms ‘nchar(x, "c")’ and ‘nchar(x, "w")’ would return
values (possibly ‘NA’) for inputs which were declared to be UTF-8 but
were not, or for invalid strings without a marked encoding in a
multi-byte locale, rather than give an error. Additional checks have
been added to mitigate this.
‘apply(a, M, function(u) c(X = ., Y = .))’ again has dimnames
containing "X" and "Y" (as in R < 3.2.0).
(Windows only) In some cases, the ‘--clean’ option to ‘R CMD INSTALL’
could fail. (PR#16178)
(Windows only) ‘choose.files()’ would occasionally include characters
from the result of an earlier call in the result of a later one.
(PR#16270)
A change in ‘RSiteSearch()’ in R 3.2.0 caused it to submit invalid
URLs. (PR#16329)
‘Rscript’ and command line ‘R’ silently ignored incomplete statements
at the end of a script; now they are reported as parse errors.
(PR#16350)
Parse data for very long strings was not stored. (PR#16354)
‘plotNode()’, the workhorse of the ‘plot’ method for ‘"dendrogram"’s is
no longer recursive, thanks to Suharto Anggono, and hence also works
for deeply nested dendrograms. (PR#15215)
The parser could overflow internally when given numbers in scientific
format with extremely large exponents. (PR#16358)
If the CRAN mirror was not set, ‘install.packages(type = "both")’ and
related functions could repeatedly query the user for it. (Part of
PR#16362)
The low-level functions ‘.rowSums()’ etc. did not check the length of
their argument, so could segfault. (PR#16367)
The ‘quietly’ argument of ‘library()’ is now correctly propagated from
‘.getRequiredPackages2()’.
Under some circumstances using the internal PCRE when building R from
source would cause external libs such as ‘-llzma’ to be omitted from
the main link.
The .Primitive default methods of the logic operators, i.e., ‘!’, ‘&’
and ‘|’, now give correct error messages when appropriate, e.g., for
‘`&`(TRUE)’ or ‘`!`()’. (PR#16385)
‘cummax(x)’ now correctly propagates ‘NA’s also when ‘x’ is of type
‘integer’ and begins with an ‘NA’.
‘summaryRprof()’ could fail when the profile contained only two
records. (PR#16395)
HTML vignettes opened using ‘vignette()’ did not support links into the
rest of the HTML help system. (Links worked properly when the vignette
was opened using ‘browseVignettes()’ or from within the help system.)
‘arima(*, xreg = .)’ (for d >= 1) computes estimated variances based on
a the number of effective observations as in R version 3.0.1 and
earlier. (PR#16278)
‘slotNames(.)’ is now correct for ‘"signature"’ objects (mostly used
internally in ‘methods’).
On some systems, the first string comparison after a locale change
would result in ‘NA’.
‘anyNA()’ gains a ‘recursive’ argument.
When ‘x’ is missing and ‘names’ is not false (including the default
value), ‘Sys.getenv(x, names)’ returns an object of class ‘"Dlist"’ and
hence prints tidily.
(Windows.) ‘shell()’ no longer consults the environment variable
‘SHELL’: too many systems have been encountered where it was set
incorrectly (usually to a path where software was compiled, not where
it was installed). ‘R_SHELL’, the preferred way to select a
non-default shell, can be used instead.
Some unusual arguments to ‘embedFonts()’ can now be specified as
character vectors, and the defaults have been changed accordingly.
Functions in the ‘Summary’ group duplicate less. (PR#15798)
(Unix-alikes.) ‘system(cmd, input = )’ now uses
‘shell-execution-environment’ redirection, which will be more natural
if ‘cmd’ is not a single command (but requires a POSIX-compliant
shell). (Wish of PR#15508)
‘read.fwf()’ and ‘read.DIF()’ gain a ‘fileEncoding’ argument, for
convenience.
Graphics devices can add attributes to their description in ‘.Device’
and ‘.Devices’. Several of those included with R use a ‘"filepath"’
attribute.
‘pmatch()’ uses hashing in more cases and so is faster at the expense
of using more memory. (PR#15697)
‘pairs()’ gains new arguments to select sets of variables to be plotted
against each other.
‘file.info(, extra_cols = FALSE)’ allows a minimal set of columns to be
computed on Unix-alikes: on some systems without properly-configured
caching this can be significantly faster with large file lists.
New function ‘dir.exists()’ in package ‘base’ to test efficiently
whether one or more paths exist and are directories.
‘dput()’ and friends gain new controls ‘hexNumeric’ and ‘digits17’
which output double and complex quantities as, respectively, binary
fractions (exactly, see ‘sprintf("%a")’) and as decimals with up to 17
significant digits.
‘save()’, ‘saveRDS()’ and ‘serialize()’ now support ‘ascii = NA’ which
writes ASCII files using ‘sprintf("%a")’ for double/complex quantities.
This is read-compatible with ‘ascii = TRUE’ but avoids
binary->decimal->binary conversions with potential loss of precision.
Unfortunately the Windows C runtime's lack of C99 compliance means that
the format cannot be read correctly there in R before 3.1.2.
The default for ‘formatC(decimal.mark =)’ has been changed to be
‘getOption("OutDec")’; this makes it more consistent with ‘format()’
and suitable for use in print methods, e.g. those for classes
‘"density"’, ‘"ecdf"’, ‘"stepfun"’ and ‘"summary.lm"’.
‘getOption("OutDec")’ is now consulted by the print method for class ‘"kmeans"’, by ‘cut()’, ‘dendrogram()’, ‘plot.ts()’ and ‘quantile()’ when constructing labels and for the report from ‘legend(trace = TRUE)’.
(In part, wish of PR#15819.)
‘printNum()’ and hence ‘format()’ and ‘formatC()’ give a warning if
‘big.mark’ and ‘decimal.mark’ are set to the same value (period and
comma are not uncommonly used for each, and this is a check that
conventions have not got mixed).
‘merge()’ can create a result which uses long vectors on 64-bit
platforms.
‘dget()’ gains a new argument ‘keep.source’ which defaults to ‘FALSE’
for speed (‘dput()’ and ‘dget()’ are most often used for data objects
where this can make ‘dget()’ many times faster).
Packages may now use a file of common macro definitions in their help
files, and may import definitions from other packages.
A number of macros have been added in the new ‘share/Rd’ directory for
use in package overview help pages, and ‘promptPackage()’ now makes use
of them.
‘tools::parse_Rd()’ gains a new ‘permissive’ argument which converts
unrecognized macros into text. This is used by
‘utils:::format.bibentry’ to allow LaTeX markup to be ignored.
‘options(OutDec =)’ can now specify a multi-byte character, e.g.,
‘options(OutDec = "\u00b7")’ in a UTF-8 locale.
‘is.recursive(x)’ is no longer true when ‘x’ is an external pointer, a
weak reference or byte code; the first enables ‘all.equal(x, x)’ when
‘x <- getClass(.)’.
‘ls()’ (aka ‘objects()’) and ‘as.list.environment()’ gain a new
argument ‘sorted’.
The ‘"source"’ attribute (which has not been added to functions by R
since before R version 2.14.0) is no longer treated as special.
Function ‘returnValue()’ has been added to give ‘on.exit()’ code access
to a function's return value for debugging purposes.
‘crossprod(x, y)’ allows more matrix coercions when ‘x’ or ‘y’ are
vectors, now equalling ‘t(x) %*% y’ in these cases (also reported by
Radford Neal). Similarly, ‘tcrossprod(x,y)’ and ‘%*%’ work in more
cases with vector arguments.
Utility function ‘dynGet()’ useful for detecting cycles, aka infinite
recursions.
The byte-code compiler and interpreter include new instructions that
allow many scalar subsetting and assignment and scalar arithmetic
operations to be handled more efficiently. This can result in
significant performance improvements in scalar numerical code.
‘apply(m, 2, identity)’ is now the same as the matrix ‘m’ when it has
_named_ row names.
A new function ‘debuggingState()’ has been added, allowing to
temporarily turn off debugging.
‘example()’ gets a new optional argument ‘run.donttest’ and
‘tools::Rd2ex()’ a corresponding ‘commentDonttest’, with a default such
that ‘example(..)’ in help examples will run ‘\donttest’ code only if
used interactively (a change in behaviour).
‘rbind.data.frame()’ gains an optional argument ‘make.row.names’, for
potential speedup.
New function ‘extSoftVersion()’ to report on the versions of
third-party software in use in this session. Currently reports
versions of ‘zlib’, ‘bzlib’, the ‘liblzma’ from ‘xz’, PCRE, ICU, TRE
and the ‘iconv’ implementation.
A similar function ‘grSoftVersion()’ in package ‘grDevices’ reports on third-party graphics software.
Function ‘tcltk::tclVersion()’ reports the Tcl/Tk version.
Calling ‘callGeneric()’ without arguments now works with primitive
generics to some extent.
‘vapply(x, FUN, FUN.VALUE)’ is more efficient notably for large
‘length(FUN.VALUE)’; as extension of PR#16061.
‘as.table()’ now allows tables with one or more dimensions of length 0
(such as ‘as.table(integer())’).
‘names(x) <- NULL’ now clears the names of call and ‘...’ objects.
‘library()’ will report a warning when an insufficient dependency
version is masking a sufficient one later on the library search path.
A new ‘plot()’ method for class ‘"raster"’ has been added.
New ‘check_packages_in_dir_changes()’ function in package ‘tools’ for
conveniently analyzing how changing sources impacts the check results
of their reverse dependencies.
Speed-up from Peter Haverty for ‘ls()’ and
‘methods:::.requirePackage()’ speeding up package loading. (PR#16133)
New ‘get0()’ function, combining ‘exists()’ and ‘get()’ in one call,
for efficiency.
‘match.call()’ gains an ‘envir’ argument for specifying the environment
from which to retrieve the ‘...’ in the call, if any; this environment
was wrong (or at least undesirable) when the ‘definition’ argument was
a function.
‘topenv()’ has been made ‘.Internal()’ for speedup, based on Peter
Haverty's proposal in PR#16140.
‘getOption()’ no longer calls ‘options()’ in the main case.
Optional use of ‘libcurl’ (version 7.28.0 from Oct 2012 or later) for
Internet access:
• ‘capabilities("libcurl")’ reports if this is available.
• ‘libcurlVersion()’ reports the version in use, and other details of the ‘"libcurl"’ build including which URL schemes it supports.
• ‘curlGetHeaders()’ retrieves the headers for ‘http://’, ‘https://’, ‘ftp://’ and ‘ftps://’ URLs: analysis of these headers can provide insights into the `existence' of a URL (it might for example be permanently redirected) and is so used in ‘R CMD check --as-cran’.
• ‘download.file()’ has a new optional method ‘"libcurl"’ which will handle more URL schemes, follow redirections, and allows simultaneous downloads of multiple URLs.
• ‘url()’ has a new method ‘"libcurl"’ which handles more URL schemes and follows redirections. The default method is controlled by a new option ‘url.method’, which applies also to the opening of URLs _via_ ‘file()’ (which happens implicitly in functions such as ‘read.table’.)
• When ‘file()’ or ‘url()’ is invoked with a ‘https://’ or ‘ftps://’ URL which the current method cannot handle, it switches to a suitable method if one is available.
(Windows.) The DLLs ‘internet.dll’ and ‘internet2.dll’ have been
merged. In this version it is safe to switch (repeatedly) between the
internal and Windows internet functions within an R session.
The Windows internet functions are still selected by flag ‘--internet2’ or ‘setInternet2()’. This can be overridden for an ‘url()’ connection _via_ its new ‘method’ argument.
‘download.file()’ has new method ‘"wininet"’, selected as the default by ‘--internet2’ or ‘setInternet2()’.
‘parent.env<-’ can no longer modify the parent of a locked namespace or
namespace imports environment. Contributed by Karl Millar.
New function ‘isNamespaceLoaded()’ for readability and speed.
‘names(env)’ now returns all the object names of an ‘environment’
‘env’, equivalently to ‘ls(env, all.names = TRUE, sorted = FALSE)’ and
also to the names of the corresponding list, ‘names(as.list(env,
all.names = TRUE))’. Note that although ‘names()’ returns a character
vector, the names have no particular ordering.
The memory manager now grows the heap more aggressively. This reduces
the number of garbage collections, in particular while data or code are
loaded, at the expense of slightly increasing the memory footprint.
New function ‘trimws()’ for removing leading/trailing whitespace.
‘cbind()’ and ‘rbind()’ now consider S4 inheritance during S3 dispatch
and also obey ‘deparse.level’.
‘cbind()’ and ‘rbind()’ will delegate recursively to ‘methods::cbind2’
(‘methods::rbind2’) when at least one argument is an S4 object and S3
dispatch fails (due to ambiguity).
(Windows.) ‘download.file(quiet = FALSE)’ now uses text rather than
Windows progress bars in non-interactive use.
New function ‘hsearch_db()’ in package ‘utils’ for building and
retrieving the help search database used by ‘help.search()’, along with
functions for inspecting the concepts and keywords in the help search
database.
New function ‘.getNamespaceInfo()’, a no-check version of
‘getNamespaceInfo()’ mostly for internal speedups.
The help search system now takes ‘\keyword’ entries in Rd files which
are not standard keywords (as given in ‘KEYWORDS’ in the R
documentation directory) as concepts. For standard keyword entries the
corresponding descriptions are additionally taken as concepts.
New ‘lengths()’ function for getting the lengths of all elements in a
list.
New function ‘toTitleCase()’ in package ‘tools’, tailored to package
titles.
The matrix methods of ‘cbind()’ and ‘rbind()’ allow matrices as inputs
which have 2^31 or more elements. (For ‘cbind()’, wish of PR#16198.)
The default method of ‘image()’ has an explicit check for a numeric or
logical matrix (which was always required).
‘URLencode()’ will not by default encode further URLs which appear to
be already encoded.
‘BIC(mod)’ and ‘BIC(mod, mod2)’ now give non-NA numbers for ‘arima()’
fitted models, as ‘nobs(mod)’ now gives the number of “used”
observations for such models. This fixes PR#16198, quite differently
than proposed there.
The ‘print()’ methods for ‘"htest"’, ‘"pairwise.htest"’ and
‘"power.htest"’ objects now have a ‘digits’ argument defaulting to (a
function of) ‘getOption("digits")’, and influencing all printed numbers
coherently. Unavoidably, this changes the display of such test results
in some cases.
Code completion for namespaces now recognizes all loaded namespaces,
rather than only the ones that are also attached.
The code completion mechanism can now be replaced by a user-specified
completer function, for (temporary) situations where the usual code
completion is inappropriate.
‘unzip()’ will now warn if it is able to detect truncation when
unpacking a file of 4GB or more (related to PR#16243).
‘methods()’ reports S4 in addition to S3 methods; output is simplified
when the ‘class’ argument is used. ‘.S3methods()’ and
‘methods::.S4methods()’ report S3 and S4 methods separately.
Higher order functions such as the ‘apply’ functions and ‘Reduce()’ now
force arguments to the functions they apply in order to eliminate
undesirable interactions between lazy evaluation and variable capture
in closures. This resolves PR#16093.
The ‘\donttest’ sections of R's help files can be tested by
‘make check TEST_DONTTEST=TRUE’ .
It is possible to request the use of system ‘valgrind’ headers _via_
‘configure’ option ‘--with-system-valgrind-headers’: note the possible
future incompatibility of such headers discussed in the 'R Installation
and Administration' manual. (Wish of PR#16068.)
The included version of ‘liblzma’ has been updated to ‘xz-utils’ 5.0.7
(minor bug fixes from 5.0.5).
‘configure’ options ‘--with-system-zlib’, ‘--with-system-bzlib’ and
‘--with-system-pcre’ are now the default. For the time being there is
fallback to the versions included in the R sources if no system
versions are found or (unlikely) if they are too old.
Linux users should check that the ‘-devel’ or ‘-dev’ versions of packages ‘zlib’, ‘bzip2’/‘libbz2’ and ‘pcre’ as well as ‘xz-devel’/‘liblzma-dev’ (or similar names) are installed.
‘configure’ by default looks for the ‘texi2any’ script from ‘texinfo’
5.1 or later, rather than the ‘makeinfo’ program. (‘makeinfo’ is a
link to the Perl script ‘texi2any’ in ‘texinfo’ 5.x.)
‘R CMD INSTALL’ gains an option ‘--built-timestamp=STAMP’ allowing 100%
reproducible package building, thanks to Dirk Eddelbuettel.
There is support for testing the ‘\dontrun’ and ‘\donttest’ parts of
examples in packages.
‘tools::testInstalledPackage()’ accepts new arguments ‘commentDontrun = FALSE’ and ‘commentDonttest = FALSE’.
‘R CMD check’ gains options ‘--run-dontrun’ and ‘--run-donttest’.
The HTML generated by ‘tools::Rd2HTML()’ and ‘tools::toHTML()’ methods
is now ‘XHTML 1.0 Strict’.
The ‘compiler’ package's utility function ‘setCompilerOptions()’ now
returns the old values invisibly. The initial optimization level can
also be set with the environment variable ‘R_COMPILER_OPTIMIZE’.
‘R CMD build’ adds a ‘NeedsCompilation’ field if one is not already
present in the ‘DESCRIPTION’ file.
‘R CMD check’ gains option ‘--test-dir’ to specify an alternative set
of tests to run.
‘R CMD check’ will now by default continue with testing after many
types of errors, and will output a summary count of errors at the end
if any have occurred.
‘R CMD check’ now checks that the ‘Title’ and ‘Description’ fields are
correctly terminated.
‘R CMD check --as-cran’ now:
• checks a ‘README.md’ file can be processed: this needs ‘pandoc’ installed.
• checks the existence and accessibility of URLs in the ‘DESCRIPTION’, ‘CITATION’, ‘NEWS.Rd’ and ‘README.md’ files and in the help files (provided the build has ‘libcurl’ support).
• reports non-ASCII characters in R source files when there is no package encoding declared in the ‘DESCRIPTION’ file.
• reports (apparent) S3 methods exported but not registered.
• reports overwriting registered S3 methods from base/recommended packages. (Such methods are replaced in the affected package for the rest of the session, even if the replacing namespace is unloaded.)
• reports if the ‘Title’ field does not appear to be in title case (see ‘Writing R Extensions’: there may be false positives, but note that technical words should be single-quoted and will then be accepted).
Most of these checks can also be selected by environment variables: see the ‘R Internals’ manual.
New C API utility ‘logspace_sum(logx[], n)’.
Entry points ‘rbinom_mu’, ‘rnbinom_mu’ and ‘rmultinom’ are remapped (by
default) to ‘Rf_rbinom_mu’ etc. This requires packages using them to
be re-installed.
‘.C(DUP = FALSE)’ and ‘.Fortran(DUP = FALSE)’ are now ignored, so
arguments are duplicated if ‘DUP = TRUE’ would do so. As their help
has long said, ‘.Call()’ is much preferred.
New entry point ‘R_allocLD’, like ‘R_alloc’ but guaranteed to have
sufficient alignment for ‘long double’ pointers.
‘isPairList()’ now returns ‘TRUE’ for DOTSXP.
Installation using external binary distributions of ‘zlib’, ‘bzip2’,
‘liblzma’, ‘pcre’, ‘libpng’, ‘jpeglib’ and ‘libtiff’ is now required,
and the build instructions have been revised.
A new ‘make’ target ‘rsync-extsoft’ has been added to obtain copies of
the external libraries from CRAN.
Building the manuals now requires ‘texi2any’ from ‘texinfo’ 5.1 or
later. CRAN binary builds include the manuals, but by default builds
from source will not, and they will be accessed from CRAN. See the
comments in ‘src/gnuwin32/MkRules.dist’ for how to specify the location
of ‘texi2any’.
(Windows) Changes have been made to support an experimental Windows
toolchain based on GCC 4.9.2. The default toolchain continues to be
based on GCC 4.6.3, as the new toolchain is not yet stable enough. A
change to a new toolchain is expected during the R 3.2.x lifetime.
(Windows) The use of macro ‘ZLIB_LIBS’ in file ‘src/Makevars.win’
(which has not been documented for a long time) now requires an
external ‘libz.a’ to be available (it is part of the ‘goodies’ used to
compile Windows binary packages). It would be simpler to use ‘-lz’
instead.
The default for option ‘pkgType’ on platforms using binary packages is
now ‘"both"’, so source packages will be tried if binary versions are
not available or not up to date.
There are options for what ‘install.packages(type = "both")’ (possibly called _via_ ‘update.packages()’) will do if compilation of a source package is desirable: see ‘?options’ (under ‘utils’).
If you intend not to accept updates as source packages, you should use ‘update.packages(type = "binary")’.
‘download.file(method = "lynx")’ is defunct.
Building R using the included versions of ‘zlib’, ‘bzip2’, ‘xz’ and
PCRE is deprecated: these are frozen (bar essential bug-fixes) and will
be removed for R 3.3.0.
The ‘configure’ option ‘--with-valgrind-instrumentation=3’ has been
withdrawn, as it did not work with recent ‘valgrind’ headers: it is now
treated as level ‘2’.
The ‘MethodsList’ class in package ‘methods’ had been deprecated in R
2.11.0 and is defunct now. Functions using it are defunct if they had
been deprecated in R 2.11.0, and are deprecated now, otherwise.
Fixed two obscure bugs in pairlist subassignment, reported by Radford
Neal as part of pqR issue 16.
Fixes for bugs in handling empty arguments and argument matching by
name in ‘log()’.
‘all.equal()’ gains methods for ‘environment’s and ‘refClass’es.
‘[<-’ and ‘[[<-’ gain S4 ‘data.frame’ methods to avoid corruption of S4
class information by the S3 methods.
‘callNextMethod()’ should now work within a ‘.local’ call when ‘...’ is
absent from ‘formals(.local)’.
‘dput(pairlist(x))’ generates a call to the ‘pairlist’ constructor
instead of the ‘list’ constructor.
Fix ‘missing()’ when arguments are propagated through ‘...’ .
(PR#15707)
‘eigen(m)’ now defaults to ‘symmetric = TRUE’ even when the dimnames
are asymmetric if the matrix is otherwise symmetric. (PR#16151)
Fix issues with forwarding ‘...’ through ‘callGeneric()’ and
‘callNextMethod()’. (PR#16141)
‘callGeneric()’ now works after a ‘callNextMethod()’.
Subclass information is kept consistent when replacing an ordinary S4
class with an “old class” _via_ the ‘S4Class’ argument to
‘setOldClass()’. Thus, for example, a ‘data.frame’ is valid for a
‘list’ argument in the signature, and a ‘factor’ is valid for ‘vector’
arguments.
In ‘qbeta()’ the inversion of ‘pbeta()’ is much more sophisticated.
This works better in corner cases some of which failed completely
previously (PR#15755), or were using too many iterations.
Auto-printing no longer duplicates objects when printing is dispatched
to a method.
‘kmeans(x, k)’ would fail when ‘nrow(x) >= 42949673’. (Comment 6 of
PR#15364)
‘Abbreviated’ locale-specific day and month names could have been
truncated in those rare locales where there are the same as the full
names.
An irrelevant warning message from updating subclass information was
silenced (the namespace would not be writable in this case).
The internal method of ‘download.file()’ can now handle files larger
than 2GB on 32-bit builds which support such files (tested on 32-bit R
running on 64-bit Windows).
‘kruskal.test()’ warns on more types of suspicious input.
The ‘as.dendrogram()’ method for ‘"hclust"’ objects gains a ‘check’
argument protecting against memory explosion for invalid inputs.
‘capabilities()’ has a new item ‘long.double’ which indicates if the
build uses a ‘long double’ type which is longer than ‘double’.
‘nlm()’ no longer modifies the callback argument in place (a new vector
is allocated for each invocation, which mimics the implicit duplication
that occurred in R < 3.1.0); note that this is a change from the
previously documented behavior. (PR#15958)
‘icuSetCollate()’ now accepts ‘locale = "ASCII"’ which uses the basic C
function ‘strcmp’ and so collates strings byte-by-byte in numerical
order.
‘sessionInfo()’ tries to report the OS version in use (not just that
compiled under, and including details of Linux distributions).
‘model.frame()’ (used by ‘lm()’ and many other modelling functions) now
warns when it drops contrasts from factors. (Wish of PR#16119)
‘install.packages()’ and friends now accept the value ‘type = "binary"’
as a synonym for the native binary type on the platform (if it has
one).
Single source or binary files can be supplied for
‘install.packages(type = "both")’ and the appropriate type and ‘repos =
NULL’ will be inferred.
New function ‘pcre_config()’ to report on some of the configuration
options of the version of PCRE in use. In particular, this reports if
regular expressions using ‘\p{xx}’ are supported.
(Windows.) ‘download.file(cacheOK = FALSE)’ is now supported when
‘internet2.dll’ is used.
‘browseURL()’ has been updated to work with Firefox 36.0 which has
dropped support for the ‘-remote’ interface.
The included version of PCRE has been updated to 8.36.
‘configure’ accepts ‘MAKEINFO=texi2any’ as another way to ensure
‘texinfo’ 5.x is used when both 5.x and 4.x are installed.
‘R CMD check’ now checks the packages used in ‘\donttest’ sections of
the examples are specified in the ‘DESCRIPTION’ file. (These are
needed to run the examples interactively.)
‘R CMD check’ checks for the undeclared use of GNU extensions in
Makefiles, and for Makefiles with a missing final linefeed.
‘R CMD build’ will correct line endings in all Makefiles, not just those in the ‘src’ directory.
‘R CMD check’ notes uses of ‘library()’ and ‘require()’ in package
code: see the section ‘Suggested packages’ of ‘Writing R Extensions’
for good practice.
The ‘configure’ option ‘--with-valgrind-instrumentation=3’ is
deprecated and will be removed in R 3.2.0.
(Windows.) ‘Rscript.exe’ was missing a manifest specifying the modern
style for common controls (e.g., the download progress bar).
If a package had extra documentation files but no vignette, the HTML
help system produced an empty index page.
The parser now gives an error if a null character is included in a
string using Unicode escapes. (PR#16046)
‘qr.Q()’ failed on complex arguments due to pre-3.0(!) typo. (PR#16054)
‘abs()’ failed with named arguments when the argument was complex.
(PR#16047)
‘"noquote"’ objects may now be used as columns in data frames.
(PR#15997)
Some values with extremely long names were printed incorrectly.
(PR#15999)
Extremely large exponents on zero expressed in scientific notation
(e.g. ‘0.0e50000’) could give ‘NaN’. (PR#15976)
‘download.file()’ reported downloaded sizes as 0KB if less than 1MB,
only for R 3.1.2 and only on big-endian platforms.
‘prompt()’ did not escape percent signs in the automatically generated
usage section of help files.
‘drop.terms()’ dropped some of the attributes of the object it was
working with. (PR#16029)
(Windows.) The command completion in ‘Rgui.exe’ messed up the console.
(PR#15791)
(Windows.) The ‘choose.files()’ command returned a blank string when
the user asked for a single file but cancelled the request. (PR#16074)
‘Math2’ S4 group generics failed to correctly dispatch ‘"structure"’-
and ‘"nonStructure"’-derived classes.
‘loadNamespace()’ imposed undocumented restrictions on the
‘versionCheck’ parameter. (Reported by Geoff Lee.)
Rare over-runs detected by AddressSanitizer in ‘substr()’ and its
replacement version have been avoided.
_Inter alia_ that fix gives the documented behaviour for ‘substr(x, 1, 2) <- ""’ (subsequently reported as PR#16214).
Loading packages incorrectly defining an S4 generic followed by a
function of the same name caused an erroneous cyclic namespace
dependency error.
Declared vignette encodings are now always passed to the vignette
engine.
Port Tomas Kalibera's fix from R-devel that restores the ‘loadMethod()’
fast path, effectively doubling the speed of S4 dispatch.
‘power.t.test()’ and ‘power.prop.test()’ now make use of the
‘extendInt’ option of ‘uniroot()’ and hence work in more extreme cases.
(PR#15792)
If a package was updated and attached when its namespace was already
loaded, it could end up with parts from one version and parts from the
other. (PR#16120)
‘tools:::.Rdconv()’ didn't accept ‘--encoding=’ due to a typo.
(PR#16121)
Unix-alike builds without a suitable ‘makeinfo’ were documented to link
the missing HTML manuals to CRAN, but did not.
‘save(*, ascii=TRUE)’ and ‘load()’ now correctly deal with ‘NaN’'s.
(PR#16137)
‘split.Date()’ retains fractional representations while avoiding
incomplete class propagation.
‘R_ext/Lapack.h’ had not been updated for changes made by LAPACK to the
argument lists of its (largely internal) functions ‘dlaed2’ and
‘dlaed3’. (PR#16157)
‘RShowDoc("NEWS", "txt")’ had not been updated for the layout changes
of R 3.1.0.
The ‘xtfrm()’ method for class ‘"Surv"’ has been corrected and its
description expanded.
‘mode(x) <- y’ would incorrectly evaluate ‘x’ before changing its mode.
(PR#16215)
‘besselJ(1, 2^64)’ and ‘besselY(..)’ now signal a warning, returning
‘NaN’ instead of typically segfaulting. (Issue 3 of PR#15554)
HTML conversion of ‘\href’ markup in ‘.Rd’ files did not remove the
backslash from ‘\%’ and so gave an invalid URL. In a related change,
the ‘\’ escape is now required in such URLs.
‘embedFonts()’ now defaults to ‘format = "ps2write"’ for ‘.ps’ and
‘.eps’ files. This is available in Ghostscript 9.x (since 2010)
whereas the previous default, ‘format = "pswrite"’, was removed in
Ghostscript 9.10.
For consistency with ‘[dpqr]norm()’, ‘[dp]lnorm(sdlog = 0)’ model a
point mass at ‘exp(mulog)’ rather than return ‘NaN’ (for an error).
‘capabilities()’ now reports if ICU is compiled in for use for
collation (it is only actually used if a suitable locale is set for
collation, and never for a ‘C’ locale).
(OS X only.) Package ‘tcltk’ checks when loaded if it is linked against
the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk component and the
X11 libraries are installed. This allows more informative error
messages to be given advising the installation of the missing component
or of XQuartz.
The ‘X11()’ device and X11-based versions of the data editor and viewer (invoked by ‘edit()’ and ‘View()’ for data frames and matrices from command-line R) check that the X11 libraries are installed and if not advises installing XQuartz.
‘icuSetCollate()’ allows ‘locale = "default"’, and ‘locale = "none"’ to
use OS services rather than ICU for collation.
Environment variable ‘R_ICU_LOCALE’ can be used to set the default ICU locale, in case the one derived from the OS locale is inappropriate (this is currently necessary on Windows).
New function ‘icuGetCollate()’ to report on the ICU collation locale in
use (if any).
‘utils::URLencode()’ was updated to use unreserved and reserved
characters from RFC 3986 (<URL: http://tools.ietf.org/html/rfc3986>)
instead of RFC 1738.
‘unique(warnings())’ and ‘c(warnings())’ are now supported.
The Bioconductor ‘version’ used by ‘setRepositories()’ now defaults to
‘3.0’. (It can be set at runtime _via_ environment variable
‘R_BIOC_VERSION’.)
Omegahat is no longer listed as providing Windows binary packages, e.g.
by ‘setRepositories()’. It has no binary packages available for R
3.1.x and those for earlier versions were 32-bit only.
The ‘configure’ script reports on the more important
capabilities/options which will not be compiled in.
More types of external BLAS are recognized by name in that report.
When building R as a shared library, the ‘-L${R_HOME}/lib${R_ARCH}’
flag is placed earlier in the link commands used during installation
and when packages are installed: this helps ensure that the current
build has priority if an R shared library has already been installed by
e.g. ‘install-libR’ in a library mentioned in ‘LDFLAGS’ (and not in
‘your system's library directory’ as documented). (Wish of PR#15790.)
LaTeX package ‘upquote’ is no longer required for R's use of
‘inconsolata’.
(Windows only) If both 32- and 64-bit versions of R are installed, the
‘bin/R.exe’ and ‘bin/Rscript.exe’ executables now run 64-bit R. (To
run 32-bit R, overwrite these files with copies of ‘bin/i386/Rfe.exe’.)
Running ‘R CMD check’ with ‘_R_CHECK_DEPENDS_ONLY_’ true now makes the
‘VignetteBuilder’ packages available even if they are listed in
‘Suggests’, since they are needed to recognise and process non-Sweave
vignettes.
‘R CMD check’ now reports empty ‘importFrom’ declarations in a
‘NAMESPACE’ file, as these are common errors (writing ‘importFrom(Pkg)’
where ‘import(Pkg)’ was intended).
‘R CMD check’ now by default checks code usage directly on the package
namespace without loading and attaching the package and its suggests
and enhances. For good practice with packages in the ‘Suggests’ field,
see §1.1.3.1 of ‘Writing R Extensions’. For use of lazy-data objects
in the package's own code, see ‘?data’.
‘dmultinom()’ did not handle non-finite probabilities correctly.
‘prettyNum(x, zero.print=*)’ now also works when ‘x’ contains ‘NA’s.
A longstanding bug exhibited by ‘nlminb()’ on Windows was traced to a
compiler bug in gcc 4.6.3; a workaround has been put in place.
(PR#15244 and PR#15914).
Rendering of ‘\command’ in HTML versions of help pages has been
improved: this is particularly evident on the help page for ‘INSTALL’.
‘as.hexmode(x)’ and ‘as.octmode(x)’ now behave correctly for some
numeric ‘x’, e.g., ‘c(NA, 1)’ or ‘c(1, pi)’.
‘drop1()’ failed if the ‘scope’ argument had no variables to drop.
(PR#15935)
‘edit()’ (and hence ‘fix()’) failed if an object had a non-character
attribute named ‘"source"’ (an attribute that had been used in R prior
to version 2.14.0).
‘callGeneric()’ could fail if the generic had ‘...’ as a formal
argument. (PR#15937).
Forking in package ‘parallel’ called C entry point ‘exit’ in the child.
This was unsafe (‘_exit’ should have been called), and could flush
‘stdin’ of the main R process (seen most often on Solaris).
As good practice, ‘stdout’ is now flushed before forking a child.
R objects such as ‘list(`a\b` = 1)’ now print correctly.
‘getAnywhere("C_pbinom")’ now returns correctly a single object (rather
than unlisting it).
The ‘confint()’ method for ‘nls()’ fits failed it these has specified
parameter limits despite using an algorithm other than ‘"port"’.
(PR#15960)
Subclassing an S4 class failed if the class required arguments to the
generator, through its ‘initialize()’ method.
‘removeSource()’ did not properly handle expressions containing
arguments that were supplied as missing, e.g. ‘x[i,]’. (PR#15957)
‘as.environment(list())’ now works, and ‘as.list()’ of such an
environment is now the same as ‘list()’. (PR#15926)
Several ‘tcltk’ functions failed when run in unusual environments.
(PR#15970)
‘options(list())’ now works (trivially). (PR#15979)
‘merge(<dendrogram>, ..)’ now works correctly for two `independent'
dendrograms (PR#15648), and still compatibly _via_ ‘adjust = "auto"’
e.g. for two branches of an existing dendrogram.
The ‘plot’ method for ‘"hclust"’ objects gets an optional argument
‘check’; when that is true (the default) it checks more carefully for
valid input.
(Windows only) If a user chose to install 64 bit R but not 32 bit R,
the ‘bin/R’ and ‘bin/Rscript’ executables failed to run. (PR#15981)
Various possible buffer overruns have been prevented, and missed memory
protection added. (PR#15990)
‘Rscript’ no longer passes ‘--args’ to ‘R’ when there are no extra
(“user”) arguments.
objects like ‘getClass("refClass")@prototype’ now ‘print()’ and ‘str()’
without error.
‘identical()’ now also looks at the S4 bit.
‘hist(x, breaks)’ is more robust in adding a small fuzz to few breaks
when some are very large. (PR#15988)
‘sub()’ and ‘gsub()’ did not handle regular expressions like ‘"\s{2,}"’
properly if the text contained ‘NA’ or non-ASCII elements in a UTF-8
locale. Part of this was due to a bug in the TRE library. (PR#16009)
‘RShowDoc("NEWS")’ now displays the PDF version.
Matrices and arrays with last dimension zero did not print at all or
incompletely. (PR#16012)
‘plot.histogram()’ and hence ‘hist()’ now respect the ‘xaxs’, ‘yaxs’
and ‘lab’ graphics parameters. (PR#16021)
‘bw.SJ(x)’ and other bw.*() no longer segfault when ‘x’ contains
non-finite values. (PR#16024)
‘R CMD Rd2pdf’ unintentionally ignored its ‘--os’ option.
The internal method of ‘download.file()’ was not reporting file sizes
and progress correctly on files larger than 2GB (inherited from
‘libxml2’). This is corrected for 64-bit builds (32-bit platforms may
not support such files, but where possible will be supported in future
versions of R).
Work around a bug in OS X Yosemite where key environment variables may
be duplicated causing issues in subprocesses. The duplicates are now
removed on R startup (_via_ Rprofile). (PR#16042)
Adjust X11 auto-launch detection in DISPLAY on OS X to recognize latest
XQuartz.
When ‘attach()’ reports conflicts, it does so compatibly with
‘library()’ by using ‘message()’.
‘R CMD Sweave’ no longer cleans any files by default, compatibly with
versions of R prior to 3.1.0. There are new options ‘--clean’,
‘--clean=default’ and ‘--clean=keepOuts’.
‘tools::buildVignette()’ and ‘tools::buildVignettes()’ with ‘clean =
FALSE’ no longer remove any created files. ‘buildvignette()’ gains a
‘keep’ argument for more cleaning customization.
The Bioconductor ‘version’ used by ‘setRepositories()’ can now be set
by environment variable ‘R_BIOC_VERSION’ at runtime, not just when R is
installed. (It has been stated that Bioconductor will switch from
‘version’ 2.14 to ‘version’ 3.0 during the lifetime of the R 3.1
series.)
Error messages from bugs in embedded ‘Sexpr’ code in Sweave documents
now report the source location.
‘type.convert()’, ‘read.table()’ and similar ‘read.*()’ functions get a
new ‘numerals’ argument, specifying how numeric input is converted when
its conversion to double precision loses accuracy. The default value,
‘"allow.loss"’ allows accuracy loss, as in R versions before 3.1.0.
For some compilers, integer addition could overflow without a warning.
R's internal code for both integer addition and subtraction is more
robust now. (PR#15774)
The function determining the default number of knots for
‘smooth.spline()’ is now exported, as ‘.nknots.smspl()’.
‘dbeta(, a,b)’, ‘pbeta()’, ‘qbeta()’ and ‘rbeta()’ are now defined also
for a = 0, b = 0, or infinite a and b (where they typically returned
‘NaN’ before).
Many package authors report that the RStudio graphics device does not
work correctly with their package's use of ‘dev.new()’. The new option
‘dev.new(noRStudioGD = TRUE)’ replaces the RStudio override by the
default device as selected by R itself, still respecting environment
variables ‘R_INTERACTIVE_DEVICE’ and ‘R_DEFAULT_DEVICE’.
‘readRDS()’ now returns visibly.
Modifying internal logical scalar constants now results in an error
instead of a warning.
‘install.packages(repos = NULL)’ now accepts ‘http://’ or ‘ftp://’ URLs
of package archives as well as file paths, and will download as
required. In most cases ‘repos = NULL’ can be deduced from the
extension of the URL.
The warning when using partial matching with the ‘$’ operator on data
frames is now only given when ‘options("warnPartialMatchDollar")’ is
‘TRUE’.
Package help requests like ‘package?foo’ now try the package ‘foo’
whether loaded or not.
General help requests now default to trying all loaded packages, not
just those on the search path.
Added a new function ‘promptImport()’, to generate a help page for a
function that was imported from another package (and presumably
re-exported, or help would not be needed).
‘configure’ option ‘--with-internal-tzcode’ can now be used with
variable ‘rsharedir’.
The included version of PCRE has been updated to 8.35.
There is a new target ‘make uninstall-libR’ to remove an installed
shared/static ‘libR’.
‘make install-libR’ now works if a sub-architecture is used, although the user will need to specify ‘libdir’ differently for different sub-architectures.
There is more extensive advice on which LaTeX packages are required to
install R or to make package manuals (as done by ‘R CMD check’) in the
‘Writing R Extensions’ manual.
Compilers/linkers were handling the visibility control in
‘src/extra/xz’ inconsistently (and apparently in some cases
incorrectly), so it has been simplified. (PR#15327)
(Windows) There is updated support for the use of ICU for collation:
see the ‘R Installation and Administration Manual’.
‘dbinom(x, n)’, ‘pbinom()’, ‘dpois()’, etc, are slightly less
restrictive in checking if ‘n’ is integer-valued. (Wish of PR#15734.)
‘pchisq(x, df, ncp, log.p = TRUE)’ is more accurate and no longer
underflows for small ‘x’ and ‘ncp < 80’, e.g, for ‘pchisq(1e-5, df =
100, ncp = 1, log = TRUE)’. (Based on PR#15635 and a suggestion by
Roby Joehanes.)
The ‘s’ (“step into”) command in the debugger would cause R to step
into expressions evaluated there, not just into functions being
debugged. (PR#15770)
The C code used by ‘strptime()’ rejected time-zone offsets of more than
‘+1200’ (‘+1245’, ‘+1300’ and ‘+1400’ can occur). (PR#15768)
(Windows only.) ‘png(type = "cairo", antialias = "gray")’ was not
accepted. (PR#15760)
Use of ‘save(..., envir=)’ with named objects could fail. (PR#15758)
‘Sweave()’ mis-parsed ‘Sexpr’ expressions that contained backslashes.
(PR#15779)
The return value from ‘options(foo = NULL)’ was not the previous value
of the option. (PR#15781)
‘enc2utf8()’ and ‘enc2native()’ did not always mark the encoding of the
return values when it was known.
‘dnbinom(x, size = <large>, mu, log = TRUE)’ no longer underflows to
-Inf for large ‘mu’, thanks to a suggestion from Alessandro Mammana
(MPI MolGen, Berlin).
‘pbeta(x, a, b, log = TRUE)’ no longer behaves discontinuously (in a
small x-region) because of denormalized numbers. Also, ‘pbeta(1-1e-12,
1e30, 1.001, log=TRUE)’ now terminates “in real time”.
The ‘"CRAN"’ filter (see ‘available.packages()’) no longer removes
duplicates other than of packages on CRAN, and does not fail if there
is no CRAN repository in ‘getOption("repos")’.
The device listing from ‘dev2bitmap()’ and ‘bitmap()’ was truncated to
1000 characters: modern versions of GhostScript on most platforms have
many more devices.
(Windows.) Commands such as ‘Sys.which()’ and ‘pipe()’ which needed to
find the full path to a command could segfault if the ‘long’ path name
was much longer than the ‘short’ path name (which ‘Sys.which()’
returns), as the behaviour of the Windows API call had changed.
‘R CMD build’ will fail with an error if one of the packages specified
in the ‘VignetteBuilder’ field is not installed. (Without loading
those packages it cannot be ascertained which files are intended to be
vignettes. This means that the ‘VignetteBuilder’ packages have to be
installed for package checking too.) (Wish of PR#15775.)
Misguided attempts to use ‘chull()’ with non-finite points now give an
error (related to PR#15777).
For a formula with exactly 32 variables the 32nd variable was aliased
to the intercept in some C-level computations of terms, so that for
example attempting to remove it would remove the intercept instead (and
leave a corrupt internal structure). (PR#15735)
‘anyDuplicated()’ silently returned wrong values when the first
duplicate was at an index which was too large to be stored in an
integer vector (although a lot of RAM and patience would have been
needed to encounter this).
‘tools::Rd2ex(commentDontrun = FALSE)’ failed if the block had only one
line.
Hexadecimal constants such as ‘0x110p-5L’ which were incorrectly
qualified by ‘L’ were parsed incorrectly since R 3.0.0, with a slightly
garbled warning. (PR#15753)
‘system()’ returned success on some platforms even if the system was
unable to launch a process. (PR#15796)
(Windows ‘Rgui’ console.) Unbuffered output was sometimes not output
immediately if the prompt was not on the last line of the console.
The built-in help server did not declare the encoding for the
‘DESCRIPTION’ or other text files to be the package encoding, so
non-ASCII characters could be displayed incorrectly.
R is now trying harder to not cleanup child processes that were not
spawned by ‘mcparallel()’ on platforms that provide information about
the source process of the ‘SIGCHLD’ signal. This allows 3rd party
libraries to manage the exit status of children that they spawn without
R interfering.
‘mcmapply()’ was only parallelizing if the number of jobs was bigger
than the number of cores. It now parallelizes if the number of jobs is
more than one.
Auto-printing would re-evaluate its argument when trying to dispatch to
a print method. This is now avoided when possible.
Unserializing (including ‘load()’ and ‘readRDS()’) could silently
return incorrect numeric values from ASCII saves if there was a read
error.
‘getParseData()’ could return incorrect values for the parents of some
elements. (Reported by Andrew Redd.)
Attempting to use data frames of 2^31 or more rows with ‘merge()’ or to
create a merged data frame of that size now gives a clearer error
message.
‘parse()’ did not check its ‘file’ argument was a connection if it was
not a character string, so e.g. ‘parse(FALSE)’ attempted to read from
‘stdin’.
Nor did ‘dump()’ and ‘dput()’.
The ‘"help.try.all.packages"’ option was ignored when the shortcut
syntax for help was used, e.g. ‘?foo’.
A potential segfault in string allocation has been fixed. (Found by
Radford Neal.)
Potential memory protection errors in ‘sort()’ and ‘D()’ have been
fixed. (Found by Radford Neal.)
Fixed a lack of error checking in graphics event functions. (Found by
Radford Neal; a different patch used here than the one in pqR.)
‘numericDeriv()’ sometimes miscalculated the gradient. (PR#15849,
reported originally by Radford Neal)
‘type.convert()’ (and hence by default ‘read.table()’) 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 version of ‘any(is.na(.))’ which is fast for
atomic vectors, 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 in several cases the time-zone database is 32-bit. For 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.
Also, a number of other changes to reduce copying of objects; all contributed by or based on suggestions by 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 execution
of 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 circles and text at extremely small sizes,
since some viewers were failing on such files.
The rightmost break for the ‘"months"’, ‘"quarters"’ and ‘"years"’
cases of ‘hist.POSIXlt()’ has been increased by a day. (Inter alia,
fixes PR#15717.)
The handling of ‘DF[i,] <- a’ where ‘i’ is of length 0 is improved.
(Inter alia, fixes PR#15718.)
‘hclust()’ gains a new method ‘"ward.D2"’ which implements Ward's
method correctly. The previous ‘"ward"’ method is ‘"ward.D"’ now, with
the old name still working. Thanks to research and proposals by Pierre
Legendre.
The ‘sunspot.month’ dataset has been amended and updated from the
official source, whereas the ‘sunspots’ and ‘sunspot.year’ datasets
will remain immutable. The documentation and source links have been
updated correspondingly.
The ‘summary()’ method for ‘"lm"’ fits warns if the fit is essentially
perfect, as most of the summary may be computed inaccurately (and with
platform-dependent values).
Programmers who use ‘summary()’ in order to extract just a component which will be reliable (e.g., ‘$cov.unscaled’) should wrap their calls in ‘suppressWarnings()’.
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. (Note that this does not currently work if a non-default
‘rsharedir’ ‘configure’ variable is used.)
(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).
The workaround of setting ‘R_OSX_VALGRIND’ has been removed: it is not
needed in current valgrind.
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)
‘model.matrix()’ assumed that the stored dimnames for a matrix was
‘NULL’ or length 2, but length 1 occurred.
The clipping region for a device was sometimes used in base graphics
before it was set.
On Windows there is support for making ‘.texi’ manuals using ‘texinfo’
5.0 or later: the setting is in file ‘src/gnuwin32/MkRules.dist’.
A packaging of the Perl script and modules for ‘texinfo’ 5.2 has been made available at <URL: http://www.stats.ox.ac.uk/pub/Rtools/>.
‘write.table()’ now handles matrices of 2^31 or more elements, for
those with large amounts of patience and disc space.
There is a new function, ‘La_version()’, to report the version of
LAPACK in use.
The HTML version of ‘An Introduction to R’ now has links to PNG
versions of the figures.
There is some support to produce manuals in ebook formats. (See
‘doc/manual/Makefile’. Suggested by Mauro Cavalcanti.)
On a Unix-alike ‘Sys.timezone()’ returns ‘NA’ if the environment
variable ‘TZ’ is unset, to distinguish it from an empty string which on
some OSes means the ‘UTC’ time zone.
The backtick may now be escaped in strings, to allow names containing
them to be constructed, e.g. ‘`\``’. (PR#15621)
‘read.table()’, ‘readLines()’ and ‘scan()’ now warn when an embedded
nul is found in the input. (Related to PR#15625 which was puzzled by
the behaviour in this unsupported case.)
(Windows only.) ‘file.symlink()’ works around the undocumented
restriction of the Windows system call to backslashes. (Wish of
PR#15631.)
‘KalmanForecast(fast = FALSE)’ is now the default, and the help
contains an example of how ‘fast = TRUE’ can be used in this version.
(The usage will change in 3.1.0.)
‘strptime()’ now checks the locale only when locale-specific formats
are used and caches the locale in use: this can halve the time taken on
OSes with slow system functions (e.g., OS X).
‘strptime()’ and the ‘format()’ methods for classes ‘"POSIXct"’,
‘"POSIXlt"’ and ‘"Date"’ recognize strings with marked encodings: this
allows, for example, UTF-8 French month names to be read on (French)
Windows.
‘iconv(to = "utf8")’ is now accepted on all platforms (some
implementations did already, but GNU ‘libiconv’ did not: however
converted strings were not marked as being in UTF-8). The official
name, ‘"UTF-8"’ is still preferred.
‘available.packages()’ is better protected against corrupt metadata
files. (A recurring problem with Debian package ‘shogun-r’: PR#14713.)
Finalizers are marked to be run at garbage collection, but run only at
a somewhat safer later time (when interrupts are checked). This
circumvents some problems with finalizers running arbitrary code during
garbage collection (the known instances being running ‘options()’ and
(C-level) ‘path.expand()’ re-entrantly).
The included version of PCRE has been updated to 8.34. This fixes bugs
and makes the behaviour closer to Perl 5.18. In particular, the
concept of ‘space’ includes ‘VT’ and hence agrees with POSIX's.
The new field ‘SysDataCompression’ in the ‘DESCRIPTION’ file allows
user control over the compression used for ‘sysdata.rda’ objects in the
lazy-load database.
‘install.packages(dependencies = value)’ for ‘value = NA’ (the default)
or ‘value = TRUE’ omits packages only in ‘LinkingTo’ for binary package
installs.
The long undocumented remapping of ‘rround()’ to ‘Rf_fround()’ in
header ‘Rmath.h’ is now formally deprecated: use ‘fround()’ directly.
Remapping of ‘prec()’ and ‘trunc()’ in the ‘Rmath.h’ header has been
disabled in C++ code (it has caused breakage with ‘libc++’ headers).
‘getParseData()’ truncated the imaginary part of complex number
constants. (Reported by Yihui Xie.)
‘dbeta(x, a, b)’ with ‘a’ or ‘b’ within a factor of 2 of the largest
representable number could infinite-loop. (Reported by Ioannis
Kosmidis.)
‘provideDimnames()’ failed for arrays with a 0 dimension. (PR#15465)
‘rbind()’ and ‘cbind()’ did not handle list objects correctly.
(PR#15468)
‘replayPlot()’ now checks if it is replaying a plot from the same
session.
‘rasterImage()’ and ‘grid.raster()’ now give error on an empty
(zero-length) raster. (Reported by Ben North.)
‘plot.lm()’ would sometimes scramble the labels in plot type 5.
(PR#15458 and PR#14837)
‘min()’ did not handle ‘NA_character_’ values properly. (Reported by
Magnus Thor Torfason.)
(Windows only.) ‘readRegistry()’ would duplicate default values for
keys. (PR#15455)
‘str(..., strict.width = "cut")’ did not handle it properly when more
than one line needed to be cut. (Reported by Gerrit Eichner.)
Removing subclass back-references when S4 classes were removed or their
namespace unloaded had several bugs (e.g., PR#15481).
‘aggregate()’ could fail when there were too many levels present in the
‘by’ argument. (PR#15004)
‘namespaceImportFrom()’ needed to detect primitive functions when
checking for duplicated imports (reported by Karl Forner).
‘getGraphicsEvent()’ did not exit when a user closed the graphics
window. (PR#15208)
Errors in vignettes were not always captured and displayed properly.
(PR#15495)
‘contour()’ could fail when dealing with extremely small z values.
(PR#15454)
Several functions did not handle zero-length vectors properly,
including ‘browseEnv()’, ‘format()’, ‘gl()’, ‘relist()’ and
‘summary.data.frame()’. (E.g., PR#15499)
‘Sweave()’ did not restore the R output to the console if it was
interrupted by a user in the middle of evaluating a code chunk.
(Reported by Michael Sumner.)
Fake installs of packages with vignettes work again.
Illegal characters in the input caused ‘parse()’ (and thus ‘source()’)
to segfault. (PR#15518)
The nonsensical use of ‘nmax = 1’ in ‘duplicated()’ or ‘unique()’ is
now silently ignored.
‘qcauchy(p, *)’ is now fully accurate even when p is very close to 1.
(PR#15521)
The ‘validmu()’ and ‘valideta()’ functions in the standard ‘glm()’
families now also report non-finite values, rather than failing.
Saved vignette results (in a ‘.Rout.save’ file) were not being compared
to the new ones during ‘R CMD check’.
Double-clicking outside of the list box (e.g., on the scrollbar) of a
Tk listbox widget generated by ‘tk_select.list()’ no longer causes the
window to close. (PR#15407)
Improved handling of edge cases in ‘parallel::splitindices()’.
(PR#15552)
HTML display of results from ‘help.search()’ and ‘??’ sometimes
contained badly constructed links.
‘c()’ and related functions such as ‘unlist()’ converted raw vectors to
invalid logical vectors. (PR#15535)
(Windows only) When a call to ‘system2()’ specified one of ‘stdin’,
‘stdout’ or ‘stderr’ to be a file, but the command was not found (e.g.,
it contained its arguments, or the program was not on the ‘PATH’), it
left the file open and unusable until R terminated. (Reported by
Mathew McLean.)
The ‘bmp()’ device was not recording ‘res = NA’ correctly: it is now
recorded as 72 ppi.
Several potential problems with compiler-specific behaviour have been
identified using the ‘Undefined Behaviour Sanitizer’ in conjunction
with the ‘clang’ compiler.
‘hcl()’ now honours ‘NA’ inputs (previously they were mapped to black).
Some translations in base packages were being looked up in the main
catalog rather than that for the package.
As a result of the 3.0.2 change about ‘the last second before the
epoch’, most conversions which should have given ‘NA’ returned that
time. (The platforms affected include Linux and OS X, but not Windows
nor Solaris.)
‘rowsum()’ has more support for matrices and data frames with 2^31 or
more elements. (PR#15587)
‘predict(<lm object>, interval = "confidence", scale = <something>)’
now works. (PR#15564)
The bug fix in 3.0.2 for PR#15411 was too aggressive, and sometimes
removed spaces that should not have been removed. (PR#15583)
Running R code in a ‘tcltk’ callback failed to set the busy flag, which
will be needed to tell OS X not to ‘App Nap’.
The code for date-times before 1902 assumed that the offset from GMT in
1902 was a whole number of minutes: that was not true of Paris (as
recorded on some platforms).
Using ‘Sys.setlocale’ to set ‘LC_NUMERIC’ to ‘"C"’ (to restore the sane
behavior) no longer gives a warning.
‘deparse()’ now deparses complex vectors in a way that re-parses to the
original values. (PR#15534, patch based on code submitted by Alex
Bertram.)
In some extreme cases (more than 10^15) integer inputs to ‘dpqrxxx()’
functions might have been rounded up by one (with a warning about being
non-integer). (PR#15624)
Plotting symbol ‘pch = 14’ had the triangle upside down on some devices
(typically screen devices). The triangle is supposed to be point up.
(Reported by Bill Venables.)
‘getSrcref()’ did not work on method definitions if
‘rematchDefinition()’ had been used.
‘KalmanForecast(fast = FALSE)’ reported a (harmless) stack imbalance.
The count of observations used by ‘KalmanRun()’ did not take missing
values into account.
In locales where the abbreviated name of one month is a partial match
for the full name of a later one, the ‘%B’ format in ‘strptime()’ could
fail. An example was French on OS X, where ‘juin’ is abbreviated to
‘jui’ and partially matches ‘juillet’. Similarly for weekday names.
‘pbeta(x, a, b, log.p = TRUE)’ sometimes underflowed to zero for very
small and very differently sized ‘a’, ‘b’. (PR#15641)
‘approx()’ and ‘approxfun()’ now handle infinite values with the
‘"constant"’ method. (PR#15655)
‘stripchart()’ again respects reversed limits in ‘xlim’ and ‘ylim’.
(PR#15664)
The ‘NEWS’ files have been re-organized.
This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y and 2.x.y releases is in files ‘NEWS.0’, ‘NEWS.1’ and ‘NEWS.2’. The latter files are now installed when R is installed. An HTML version of news from 2.10.0 to 2.15.3 is available as ‘doc/html/NEWS.2.html’.
‘sum()’ for integer arguments now uses an integer accumulator of at
least 64 bits and so will be more accurate in the very rare case that a
cumulative sum exceeds 2^53 (necessarily summing more than 4 million
elements).
The ‘example()’ and ‘tools::Rd2ex()’ functions now have parameters to
allow them to ignore ‘\dontrun’ markup in examples. (Suggested by
Peter Solymos.)
‘str(x)’ is considerably faster for very large lists, or factors with
100,000 levels, the latter as in PR#15337.
‘col2rgb()’ now converts factors to character strings not integer codes
(suggested by Bryan Hanson).
‘tail(warnings())’ now works, _via_ the new ‘`[`’ method.
There is now support for the LaTeX style file ‘zi4.sty’ which has in
some distributions replaced ‘inconsolata.sty’.
‘unlist(x)’ now typically returns all non-list ‘x’s unchanged, not just
the “vector” ones. Consequently, ‘format(lst)’ now also works when the
list ‘lst’ has non-vector elements.
The ‘tools::getVignetteInfo()’ function has been added to give
information about installed vignettes.
New ‘assertCondition()’, etc. utilities in ‘tools’, useful for testing.
Profiling now records non-inlined calls from byte-compiled code to
‘BUILTIN’ functions.
Various functions in ‘stats’ and elsewhere that use non-standard
evaluation are now more careful to follow the namespace scoping rules.
E.g., ‘stats::lm()’ can now find ‘stats::model.frame()’ even if ‘stats’
is not on the search path or if some package defines a function of that
name.
If an invalid/corrupt ‘.Random.seed’ object is encountered in the
workspace it is ignored with a warning rather than giving an error.
(This allows R itself to rely on a working RNG, e.g. to choose a random
port.)
‘seq()’ and ‘seq.int()’ give more explicit error messages if called
with invalid (e.g., ‘NaN’) inputs.
When ‘parse()’ finds a syntax error, it now makes partial parse
information available up to the location of the error. (Request of
Reijo Sund.)
Methods invoked by ‘NextMethod()’ had a different dynamic parent to the
generic. This was causing trouble where S3 methods invoked _via_ lazy
evaluation could lose track of their generic. (PR#15267)
Code for the negative binomial distribution now treats the case ‘size
== 0’ as a one-point distribution at zero.
‘abbreviate()’ handles without warning non-ASCII input strings which
require no abbreviation.
‘read.dcf()’ no longer has a limit of 8191 bytes per line. (Wish of
PR#15250.)
‘formatC(x)’ no longer copies the class of ‘x’ to the result, to avoid
misuse creating invalid objects as in PR#15303. A warning is given if
a class is discarded.
Dataset ‘npk’ has been copied from ‘MASS’ to allow more tests to be run
without recommended packages being installed.
The initialization of the regression coefficients for non-degenerate
differenced models in ‘arima()’ has been changed and in some examples
avoids a local maximum. (PR#15396)
‘termplot()’ now has an argument ‘transform.x’ to control the display
of individual terms in the plot. (PR#15329)
‘format()’ now supports ‘digits = 0’, to display ‘nsmall’ decimal
places.
There is a new read-only ‘par()’ parameter called ‘"page"’, which
returns a logical value indicating whether the next ‘plot.new()’ call
will start a new page.
Processing Sweave and Rd documents to PDF now renders backticks and
single quotes better in several instances, including in ‘\code’ and
‘\samp’ expressions.
‘utils::modifyList()’ gets a new argument ‘keep.null’ allowing ‘NULL’
components in the replacement to be retained, instead of causing
corresponding components to be deleted.
‘tools::pkgVignettes()’ gains argument ‘check’; if set to ‘TRUE’, it
will warn when it appears a vignette requests a non-existent vignette
engine.
‘R CMD check --as-cran’ checks the line widths in usage and examples
sections of the package Rd files.
‘R CMD check --as-cran’ now implies ‘--timings’.
‘R CMD check’ looks for command ‘gfile’ if a suitable ‘file’ is not
found. (Although ‘file’ is not from GNU, OpenCSW on Solaris installs
it as ‘gfile’.)
‘R CMD build’ (with the internal ‘tar’) checks the permissions of
‘configure’ and ‘cleanup’ files and adds execute permission to the
recorded permissions for these files if needed, with a warning. This
is useful on OSes and file systems which do not support execute
permissions (notably, on Windows).
‘R CMD build’ now weaves and tangles all vignettes, so suggested
packages are not required during package installation if the source
tarball was prepared with current ‘R CMD build’.
‘checkFF()’ (used by ‘R CMD check’) does a better job of detecting
calls from other packages, including not reporting those where a
function has been copied from another namespace (e.g., as a default
method). It now reports calls where ‘.NAME’ is a symbol registered in
another package.
On Unix-alike systems, ‘R CMD INSTALL’ now installs packages group
writably whenever the library (‘lib.loc’) is group writable. Hence,
‘update.packages()’ works for other group members (suggested originally
and from a patch by Dirk Eddelbuettel).
‘R CMD javareconf’ now supports the use of symbolic links for
‘JAVA_HOME’ on platforms which have ‘realpath’. So it is now possible
to use
R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-1.7.0
on a Linux system and record that value rather than the frequently-changing full path such as ‘/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64’.
(Windows only.) ‘Rscript -e’ requires a non-empty argument for
consistency with Unix versions of R. (Also ‘Rterm -e’ and ‘R -e’.)
‘R CMD check’ does more thorough checking of declared packages and
namespaces. It reports
• packages declared in more than one of the ‘Depends’, ‘Imports’, ‘Suggests’ and ‘Enhances’ fields of the ‘DESCRIPTION’ file.
• namespaces declared in ‘Imports’ but not imported from, neither in the ‘NAMESPACE’ file nor using the ‘::’ nor ‘:::’ operators.
• packages which are used in ‘library()’ or ‘requires()’ calls in the R code but were already put on the search path _via_ ‘Depends’.
• packages declared in ‘Depends’ not imported _via_ the ‘NAMESPACE’ file (except the standard packages). Objects used from ‘Depends’ packages should be imported to avoid conflicts and to allow correct operation when the namespace is loaded but not attached.
• objects imported _via_ ‘:::’ calls where ‘::’ would do.
• objects imported by ‘::’ which are not exported.
• objects imported by ‘:::’ calls which do not exist.
See ‘Writing R Extensions’ for good practice.
‘R CMD check’ optionally checks for non-standard top-level files and
directories (which are often mistakes): this is enabled for
‘--as-cran’.
LaTeX style file ‘upquote.sty’ is no longer included (the version was
several years old): it is no longer used in R. A much later version is
commonly included in LaTeX distributions but does not play well with
the ‘ae’ fonts which are the default for Sweave vignettes.
‘R CMD build’ makes more use of the ‘build’ sub-directory of package
sources, for example to record information about the vignettes.
‘R CMD check’ analyses ‘:::’ calls.
The macros used for the texinfo manuals have been changed to work
better with the incompatible changes made in ‘texinfo 5.x’.
The minimum version for a system ‘xz’ library is now 5.0.3 (was 4.999).
This is in part to avoid 5.0.2, which can compress in ways other
versions cannot decompress.
The included version of PCRE has been updated to 8.33.
The included version of ‘zlib’ has been updated to 1.2.8, a bug-fix
release.
The included version of xz utils's ‘liblzma’ has been updated to 5.0.5.
Since ‘javareconf’ (see above) is used when R is installed, a stable
link for ‘JAVA_HOME’ can be supplied then.
Configuring with ‘--disable-byte-compilation’ will override the
‘DESCRIPTION’ files of recommended packages, which typically require
byte-compilation.
More of the installation and checking process will work even when
‘TMPDIR’ is set to a path containing spaces, but this is not
recommended and external software (such as ‘texi2dvi’) may fail.
Installation is aborted immediately if a ‘LinkingTo’ package is not
installed.
‘R CMD INSTALL’ has a new option ‘--no-byte-compile’ which will
override a ‘ByteCompile’ field in the package's ‘DESCRIPTION’ file.
License ‘BSD’ is deprecated: use ‘BSD_3_clause’ or ‘BSD_2_clause’
instead.
License ‘X11’ is deprecated: use ‘MIT’ or ‘BSD_2_clause’ instead.
Version requirements for ‘LinkingTo’ packages are now recognized: they
are checked at installation. (Fields with version requirements were
previously silently ignored.)
The limit of 500 ‘S3method’ entries in a ‘NAMESPACE’ file has been
removed.
The default ‘version’ of Bioconductor for its packages has been changed
to the upcoming ‘2.13’, but this can be set by the environment variable
‘R_BIOC_VERSION’ when R is installed.
‘Rdefines.h’ has been tweaked so it can be included in C++ code after
‘R_ext/Boolean.h’ (which is included by ‘R.h’).
Note that ‘Rdefines.h’ is not kept up-to-date, and ‘Rinternals.h’ is preferred for new code.
‘eval’ and ‘applyClosure’ are now protected against package code
supplying an invalid ‘rho’.
The unused ‘namespace’ argument to ‘package.skeleton()’ is now formally
deprecated and will be removed in R 3.1.0.
‘plclust()’ is deprecated: use the ‘plot()’ method for class ‘"hclust"’
instead.
Functions ‘readNEWS()’ and ‘checkNEWS()’ in package ‘tools’ are
deprecated (and they have not worked with current ‘NEWS’ files for a
long time).
‘An Introduction to R’ has a new chapter on using R as a scripting
language including interacting with the OS.
‘help.request()’ could not determine the current version of R on CRAN.
(PR#15241)
On Windows, ‘file.info()’ failed on root directories unless the path
was terminated with an explicit ‘"."’. (PR#15302)
The ‘regmatches<-()’ replacement function mishandled results coming
from ‘regexpr()’. (PR#15311)
The help for ‘setClass()’ and ‘representation()’ still suggested the
deprecated argument ‘representation=’. (PR#15312)
‘R CMD config’ failed in an installed build of R 3.0.1 (only) when a
sub-architecture was used. (Reported by Berwin Turlach.)
On Windows, the installer modified the ‘etc/Rconsole’ and
‘etc/Rprofile.site’ files even when default options were chosen, so the
MD5 sums did not refer to the installed versions. (Reported by Tal
Galili.)
‘plot(hclust(), cex =)’ respects ‘cex’ again (and possibly others
similarly). (Reported by Peter Langfelder.)
If multiple packages were checked by ‘R CMD check’, and one was written
for a different OS, it would set ‘--no-install’ for all following
packages as well as itself.
‘qr.coef()’ and related functions did not properly coerce real vectors
to complex when necessary. (PR#15332)
‘ftable(a)’ now fixes up empty ‘dimnames’ such that the result is
printable.
‘package.skeleton()’ was not starting its search for function objects
in the correct place if ‘environment’ was supplied. (Reported by Karl
Forner.)
Parsing code was changing the length field of vectors and confusing the
memory manager. (PR#15345)
The Fortran routine ‘ZHER2K’ in the reference BLAS had a comment-out
bug in two places. This caused trouble with ‘eigen()’ for Hermitian
matrices. (PR#15345 and report from Robin Hankin)
‘vignette()’ and ‘browseVignettes()’ did not display non-Sweave
vignettes properly.
Two warning/error messages have been corrected: the (optional) warning
produced by a partial name match with a pairlist, the error message
from a zero-length argument to the ‘:’ operator. (Found by Radford
Neal; PR#15358, PR#15356)
‘svd()’ returned ‘NULL’ rather than omitting components as documented.
(Found by Radford Neal; PR#15360)
‘mclapply()’ and ‘mcparallel()’ with ‘silent = TRUE’ could break a
process that uses ‘stdout’ output unguarded against broken pipes (e.g.,
‘zip’ will fail silently). To work around such issues, they now replace
‘stdout’ with a descriptor pointed to ‘/dev/null’ instead. For this
purpose, internal ‘closeStdout’ and ‘closeStderr’ functions have gained
the ‘to.null’ flag.
‘log()’, ‘signif()’ and ‘round()’ now raise an error if a single named
argument is not named ‘x’. (PR#15361)
‘deparse()’ now deparses raw vectors in a form that is syntactically
correct. (PR#15369)
The ‘jpeg’ driver in Sweave created a JPEG file, but gave it a ‘.png’
extension. (PR#15370)
Deparsing of infix operators with named arguments is improved.
(PR#15350)
‘mget()’, ‘seq.int()’ and ‘numericDeriv()’ did not duplicate arguments
properly. (PR#15352, PR#15353, PR#15354)
‘kmeans(algorithm = "Hartigan-Wong")’ now always stops iterating in the
QTran stage. (PR#15364).
‘read.dcf()’ re-allocated incorrectly and so could segfault when called
on a file with lines of more than 100 bytes.
On systems where ‘mktime()’ does not set ‘errno’, the last second
before the epoch could not be converted from ‘POSIXlt’ to ‘POSIXct’.
(Reported by Bill Dunlap.)
‘add1.glm()’ miscalculated F-statistics when df > 1. (Bill Dunlap,
PR#15386).
‘stem()’ now discards infinite inputs rather than hanging. (PR#15376)
The parser now enforces C99 syntax for floating point hexadecimal
constants (e.g., ‘0x1.1p0’), rather than returning unintended values
for malformed constants. (PR#15234)
‘model.matrix()’ now works with very long LHS names (more than 500
bytes). (PR#15377)
‘integrate()’ reverts to the pre-2.12.0 behaviour: from 2.12.0 to 3.0.1
it sometimes failed to achieve the requested tolerance and reported
error estimates that were exceeded. (PR#15219)
‘strptime()’ now handles ‘%W’ fields with value 0. (PR#15915)
R is now better protected against people trying to interact with the
console in startup code. (PR#15325)
Subsetting 1D arrays often lost dimnames (PR#15301).
Unary ‘+’ on a logical vector did not coerce to integer, although unary
‘-’ did.
‘na.omit()’ and ‘na.exclude()’ added a row to a zero-row data frame.
(PR#15399)
All the (where necessary cut-down) vignettes are installed if R was
configured with ‘--without-recommended-packages’.
‘source()’ did not display filenames when reporting syntax errors.
Syntax error reports misplaced the caret pointing out the bad token.
(Windows only) Starting R with ‘R’ (instead of ‘Rterm’ or ‘Rgui’) would
lose any zero-length strings from the command line arguments.
(PR#15406)
Errors in the encoding specified on the command line _via_
‘--encoding=foo’ were not handled properly. (PR#15405)
If ‘x’ is a symbol, ‘is.vector(x, "name")’ now returns ‘TRUE’, since
‘"name"’ and ‘"symbol"’ should be synonyms. (Reported by Hervé Pagès.)
‘R CMD rtags’ works on platforms (such as OS X) with a XSI-conformant
shell command ‘echo’. (PR#15231)
‘is.unsorted(NA)’ returns false as documented (rather than ‘NA’).
‘R CMD LINK’ did not know about sub-architectures.
‘system()’ and ‘system2()’ are better protected against users who
misguidedly have spaces in the temporary directory path.
‘file.show()’ and ‘edit()’ are now more likely to work on file paths
containing spaces. (Where external utilities are used, not the norm on
Windows nor in ‘R.app’ which should previously have worked.)
Packages using the ‘methods’ package are more likely to work when they
import it but it is not attached. (Several parts of its C code were
looking for its R functions on the search path rather than in its
namespace.)
‘lgamma(-x)’ is no longer ‘NaN’ for very small x.
(Windows) ‘system2()’ now respects specifying ‘stdout’ and ‘stderr’ as
files if called from ‘Rgui’. (PR#15393)
Closing an ‘x11()’ device whilst ‘locator()’ or ‘identify()’ is in
progress no longer hangs R. (PR#15253)
‘list.dirs(full.names = FALSE)’ was not implemented. (PR#15170)
‘format()’ sometimes added unnecessary spaces. (PR#15411)
‘all.equal(check.names = FALSE)’ would ignore the request to ignore the
names and would check them as attributes.
The symbol set by ‘tools::Rd2txt_options(itemBullet=)’ was not
respected in some locales. (PR#15435)
‘mcMap()’ was not exported by package ‘parallel’. (PR#15439)
‘plot()’ for ‘TukeyHSD’ objects did not balance ‘dev.hold()’ and
‘dev.flush()’ calls on multi-page plots. (PR#15449)
‘chooseCRANmirror()’ and ‘chooseBioCmirror()’ gain an ‘ind’ argument
(like ‘setRepositories()’).
‘mcparallel’ has a new argument ‘mc.interactive’ which can modify the
interactive flag in the child process. The new default is ‘FALSE’ which
makes child processes non-interactive by default (this prevents
lock-ups due to children waiting for interactive input).
‘scan()’ now warns when end-of-file occurs within a quoted string.
‘count.fields()’ is now consistent with ‘scan()’ in its handling of
newlines in quoted strings. Instead of triggering an error, this
results in the current line receiving ‘NA’ as the field count, with the
next line getting the total count of the two lines.
The default method of ‘image()’ will plot axes of the class of ‘xlim’
and ‘ylim’ (and hence of ‘x’ and ‘y’ if there is a suitable ‘range()’
method). Based on a suggestion of Michael Sumner.
‘load()’ now has a ‘verbose’ argument for debugging support, to print
the names of objects just before loading them.
When loading a serialized object encounters a reference to a namespace
which cannot be loaded, this is replaced by a reference to the global
environment, with a warning.
‘pairs()’ gains a ‘line.main’ option for title placement.
The remaining instances in which serialization to a raw vector was
limited to 2GB have been unlimited on a 64-bit platform, and in most
cases serialization to a vector of more than 1GB will be substantially
faster.
‘R CMD config’ now make use of personal ‘Makevars’ files under ‘~/.R’
and a site file ‘Makevars.site’, in the same way as ‘R CMD SHLIB’ and
‘R CMD INSTALL’. This makes the utility more useful in package
‘configure’ scripts.
On Windows finding the personal files may require the environment variable ‘HOME’ set.
The old behaviour can be obtained with the new options ‘--no-user-files’ and ‘--no-site-files’.
Alternatives to the site and user customization files ‘Makevars.site’
and ‘~/.R/Makevars’ can be specified _via_ the environment variables
‘R_MAKEVARS_SITE’ and ‘R_MAKEVARS_USER’ respectively. These can be
used to suppress the use of the default files by setting an empty value
(where possible) or a non-existent path.
‘sys.source()’ did not report error locations when ‘keep.source =
TRUE’.
‘as.POSIXct.numeric’ was coercing ‘origin’ using the ‘tz’ argument and
not ‘"GMT"’ as documented (PR#14973).
The active binding to assign fields in reference classes has been
cleaned up to reduce dependence on the class' package environment, also
fixing bug in initializing read-only fields (inspired by a report from
Hadley Wickham).
‘str(d)’ no longer gives an error when ‘names(d)’ contain illegal
multibyte strings (PR#15247).
Profiling of built-in functions with ‘line.profiling= TRUE’ did not
record the line from which they were called.
‘citation(pkg)’ dropped the header and footer specified in the
‘CITATION’ file (PR#15257).
Quotes were handled differently when reading the first line and reading
the rest, so ‘read.table()’ misread some files that contained quote
characters (PR#15245).
‘cat()’ with ‘sep’ a character vector of length greater than one and
more than one argument was using separators inconsistently (PR#15261).
On Windows in R 3.0.0, ‘savePlot()’ failed because of an incorrect
check on the argument count.
‘unzip(list = TRUE)’ returned ‘Names’ as a factor and not a character
vector (as documented) for the internal method. (Noticed by Sean
O'Riordain.)
‘contourLines()’ now checks more comprehensively for conformance of its
‘x’, ‘y’ and ‘z’ arguments (it was used incorrectly in package ‘R2G2’).
Saved graphics display lists are R version-specific. Attempting to
load workspaces containing them (or some other version-specific
objects) aborted the load in R 3.0.0 and earlier; now it does a partial
load and generates a warning instead.
In R 3.0.0, ‘identify()’ and ‘locator()’ did not record information
correctly, so replaying a graph (e.g., by copying it to another device)
would fail. (PR#15271)
Calling ‘file.copy()’ or ‘dirname()’ with the invalid input ‘""’ (which
was being used in packages, despite not being a file path) could have
caused a segfault.
‘dirname("")’ is now ‘""’ rather than ‘"."’ (unless it segfaulted).
‘supsmu()’ could read/write outside its input vectors for very short
inputs (seen in package ‘rms’ for ‘n = 4’).
‘as.dendrogram()’'s ‘hclust’ method uses less memory and hence gets
considerably faster for large (n ~ 1000) clusterings, thanks to Daniel
Müllner. (PR#15174)
The return value when all workers failed from
‘parallel::mclapply(mc.preschedule = TRUE)’ was a list of strings and
not of error objects. (Spotted by Karl Forner and Bernd Bischl.)
In R 3.0.0, when ‘help()’ found multiple pages with the same alias, the
HTML display of all the selections was not produced. (PR#15282)
‘splinefun(method="monoH.FC")’ now produces a function with first
argument named ‘x’ and allows ‘deriv=3’, as documented. (PR#15273)
‘summaryRprof()’ would only read the first ‘chunksize’ lines of an
‘Rprof’ file produced with ‘line.profiling=TRUE’. By default, this is
the first 100 seconds. (PR#15288)
‘lsfit()’ produced an incorrect error message when argument ‘x’ had
more columns than rows or ‘x’ had a different number of rows than ‘y’.
(Spotted by Renaud Gaujoux.)
Binary operations on equal length vectors copied the class name from
the second operand when the first had no class name, but did not set
the object bit. (PR#15299)
The ‘trace()’ method for reference generator objects failed after those
objects became function definitions.
‘write.table()’ did not check that factors were constructed correctly,
and so caused a segment fault when writing bad ones. (PR#15300)
The internal HTTP server no longer chokes on POST requests without
body. It will also pass-through other request types for custom handlers
(with the method stored in Request-Method header) instead of failing.
Packages need to be (re-)installed under this version (3.0.0) of R.
There is a subtle change in behaviour for numeric index values 2^31 and
larger. These never used to be legitimate and so were treated as ‘NA’,
sometimes with a warning. They are now legal for long vectors so there
is no longer a warning, and ‘x[2^31] <- y’ will now extend the vector
on a 64-bit platform and give an error on a 32-bit one.
It is now possible for 64-bit builds to allocate amounts of memory
limited only by the OS. It may be wise to use OS facilities (e.g.,
‘ulimit’ in a ‘bash’ shell, ‘limit’ in ‘csh’), to set limits on overall
memory consumption of an R process, particularly in a multi-user
environment. A number of packages need a limit of at least 4GB of
virtual memory to load.
64-bit Windows builds of R are by default limited in memory usage to the amount of RAM installed: this limit can be changed by command-line option ‘--max-mem-size’ or setting environment variable ‘R_MAX_MEM_SIZE’.
Negative numbers for colours are consistently an error: previously they
were sometimes taken as transparent, sometimes mapped into the current
palette and sometimes an error.
‘identical()’ has a new argument, ‘ignore.environment’, used when
comparing functions (with default ‘FALSE’ as before).
There is a new option, ‘options(CBoundsCheck=)’, which controls how
‘.C()’ and ‘.Fortran()’ pass arguments to compiled code. If true
(which can be enabled by setting the environment variable
‘R_C_BOUNDS_CHECK’ to ‘yes’), raw, integer, double and complex
arguments are always copied, and checked for writing off either end of
the array on return from the compiled code (when a second copy is
made). This also checks individual elements of character vectors
passed to ‘.C()’.
This is not intended for routine use, but can be very helpful in finding segfaults in package code.
In ‘layout()’, the limits on the grid size have been raised (again).
New simple ‘provideDimnames()’ utility function.
Where methods for ‘length()’ return a double value which is
representable as an integer (as often happens for package ‘Matrix’),
this is converted to an integer.
Matrix indexing of data frames by two-column numeric indices is now
supported for replacement as well as extraction.
‘setNames()’ now has a default for its ‘object’ argument, useful for a
character result.
‘StructTS()’ has a revised additive constant in the ‘loglik’ component
of the result: the previous definition is returned as the ‘loglik0’
component. However, the help page has always warned of a lack of
comparability of log-likelihoods for non-stationary models. (Suggested
by Jouni Helske.)
The logic in ‘aggregate.formula()’ has been revised. It is now
possible to use a formula stored in a variable; previously, it had to
be given explicitly in the function call.
‘install.packages()’ has a new argument ‘quiet’ to reduce the amount of
output shown.
Setting an element of the graphics argument ‘lwd’ to a negative or
infinite value is now an error. Lines corresponding to elements with
values ‘NA’ or ‘NaN’ are silently omitted.
Previously the behaviour was device-dependent.
Setting graphical parameters ‘cex’, ‘col’, ‘lty’, ‘lwd’ and ‘pch’ in
‘par()’ now requires a length-one argument. Previously some silently
took the first element of a longer vector, but not always when
documented to do so.
‘Sys.which()’ when used with inputs which would be unsafe in a shell
(e.g., absolute paths containing spaces) now uses appropriate quoting.
‘as.tclObj()’ has been extended to handle raw vectors. Previously, it
only worked in the other direction. (Contributed by Charlie
Friedemann, PR#14939.)
New functions ‘cite()’ and ‘citeNatbib()’ have been added, to allow
generation of in-text citations from ‘"bibentry"’ objects. A ‘cite()’
function may be added to ‘bibstyle()’ environments.
A ‘sort()’ method has been added for ‘"bibentry"’ objects.
The ‘bibstyle()’ function now defaults to setting the default
bibliography style. The ‘getBibstyle()’ function has been added to
report the name of the current default style.
‘scatter.smooth()’ now has an argument ‘lpars’ to pass arguments to
‘lines()’.
‘pairs()’ has a new ‘log’ argument, to allow some or all variables to
be plotted on logarithmic scale. (In part, wish of PR#14919.)
‘split()’ gains a ‘sep’ argument.
‘termplot()’ does a better job when given a model with interactions
(and no longer attempts to plot interaction terms).
The parser now incorporates code from Romain Francois' ‘parser’
package, to support more detailed computation on the code, such as
syntax highlighting, comment-based documentation, etc. Functions
‘getParseData()’ and ‘getParseText()’ access the data.
There is a new function ‘rep_len()’ analogous to ‘rep.int()’ for when
speed is required (and names are not).
The undocumented use ‘rep(NULL, length.out = n)’ for ‘n > 0’ (which
returns ‘NULL’) now gives a warning.
‘demo()’ gains an ‘encoding’ argument for those packages with non-ASCII
demos: it defaults to the package encoding where there is one.
‘strwrap()’ converts inputs with a marked encoding to the current
locale: previously it made some attempt to pass through as bytes inputs
invalid in the current locale.
Specifying both ‘rate’ and ‘scale’ to ‘[dpqr]gamma’ is a warning (if
they are essentially the same value) or an error.
‘merge()’ works in more cases where the data frames include matrices.
(Wish of PR#14974.)
‘optimize()’ and ‘uniroot()’ no longer use a shared parameter object
across calls. (‘nlm()’, ‘nlminb()’ and ‘optim()’ with numerical
derivatives still do, as documented.)
The ‘all.equal()’ method for date-times is now documented: times are
regarded as equal (by default) if they differ by up to 1 msec.
‘duplicated()’ and ‘unique()’ gain a ‘nmax’ argument which can be used
to make them much more efficient when it is known that there are only a
small number of unique entries. This is done automatically for
factors.
Functions ‘rbinom()’, ‘rgeom()’, ‘rhyper()’, ‘rpois()’, ‘rnbinom(),’
‘rsignrank()’ and ‘rwilcox()’ now return integer (not double) vectors.
This halves the storage requirements for large simulations.
‘sort()’, ‘sort.int()’ and ‘sort.list()’ now use radix sorting for
factors of less than 100,000 levels when ‘method’ is not supplied. So
does ‘order()’ if called with a single factor, unless ‘na.last = NA’.
‘diag()’ as used to generate a diagonal matrix has been re-written in C
for speed and less memory usage. It now forces the result to be
numeric in the case ‘diag(x)’ since it is said to have ‘zero
off-diagonal entries’.
‘backsolve()’ (and ‘forwardsolve()’) are now internal functions, for
speed and support for large matrices.
More matrix algebra functions (e.g., ‘chol()’ and ‘solve()’) accept
logical matrices (and coerce to numeric).
‘sample.int()’ has some support for n >= 2^31: see its help for the
limitations.
A different algorithm is used for ‘(n, size, replace = FALSE, prob = NULL)’ for ‘n > 1e7’ and ‘size <= n/2’. This is much faster and uses less memory, but does give different results.
‘approxfun()’ and ‘splinefun()’ now return a wrapper to an internal
function in the ‘stats’ namespace rather than a ‘.C()’ or ‘.Call()’
call. This is more likely to work if the function is saved and used in
a different session.
The functions ‘.C()’, ‘.Call()’, ‘.External()’ and ‘.Fortran()’ now
give an error (rather than a warning) if called with a named first
argument.
‘Sweave()’ by default now reports the locations in the source file(s)
of each chunk.
‘clearPushBack()’ is now a documented interface to a long-existing
internal call.
‘aspell()’ gains filters for R code, Debian Control Format and message
catalog files, and support for R level dictionaries. In addition,
package ‘utils’ now provides functions ‘aspell_package_R_files()’ and
‘aspell_package_C_files()’ for spell checking R and C level message
strings in packages.
‘bibentry()’ gains some support for “incomplete” entries with a
‘crossref’ field.
‘gray()’ and ‘gray.colors()’ finally allow ‘alpha’ to be specified.
‘monthplot()’ gains parameters to control the look of the reference
lines. (Suggestion of Ian McLeod.)
Added support for new ‘%~%’ relation (“is distributed as”) in plotmath.
‘domain = NA’ is accepted by ‘gettext()’ and ‘ngettext()’, analogously
to ‘stop()’ etc.
‘termplot()’ gains a new argument ‘plot = FALSE’ which returns
information to allow the plots to be modified for use as part of other
plots, but does not plot them. (Contributed by Terry Therneau,
PR#15076.)
‘quartz.save()’, formerly an undocumented part of ‘R.app’, is now
available to copy a device to a ‘quartz()’ device. ‘dev.copy2pdf()’
optionally does this for PDF output: ‘quartz.save()’ defaults to PNG.
The default method of ‘pairs()’ now allows ‘text.panel = NULL’ and the
use of ‘<foo>.panel = NULL’ is now documented.
‘setRefClass()’ and ‘getRefClass()’ now return class generator
functions, similar to ‘setClass()’, but still with the reference fields
and methods as before (suggestion of Romain Francois).
New functions ‘bitwNot()’, ‘bitwAnd()’, ‘bitwOr()’ and ‘bitwXor()’,
using the internal interfaces previously used for classes ‘"octmode"’
and ‘"hexmode"’.
Also ‘bitwShiftL()’ and ‘bitwShiftR()’ for shifting bits in elements of integer vectors.
New option ‘"deparse.cutoff"’ to control the deparsing of language
objects such as calls and formulae when printing. (Suggested by a
comment of Sarah Goslee.)
‘colors()’ gains an argument ‘distinct’.
New ‘demo(colors)’ and ‘demo(hclColors)’, with utility functions.
‘list.files()’ (aka ‘dir()’) gains a new optional argument ‘no..’ which
allows to exclude ‘"."’ and ‘".."’ from listings.
Multiple time series are also of class ‘"matrix"’; consequently,
‘head()’, e.g., is more useful.
‘encodeString()’ preserves UTF-8 marked encodings. Thus if factor
levels are marked as UTF-8 an attempt is made to print them in UTF-8 in
‘RGui’ on Windows.
‘readLines()’ and ‘scan()’ (and hence ‘read.table()’) in a UTF-8 locale
now discard a UTF-8 byte-order-mark (BOM). Such BOMs are allowed but
not recommended by the Unicode Standard: however Microsoft applications
can produce them and so they are sometimes found on websites.
The encoding name ‘"UTF-8-BOM"’ for a connection will ensure that a UTF-8 BOM is discarded.
‘mapply(FUN, a1, ..)’ now also works when ‘a1’ (or a further such
argument) needs a ‘length()’ method (which the documented arguments
never do). (Requested by Hervé Pagès; with a patch.)
‘.onDetach()’ is supported as an alternative to ‘.Last.lib’. Unlike
‘.Last.lib’, this does not need to be exported from the package's
namespace.
The ‘srcfile’ argument to ‘parse()’ may now be a character string, to
be used in error messages.
The ‘format()’ method for ‘ftable’ objects gains a ‘method’ argument,
propagated to ‘write.ftable()’ and ‘print()’, allowing more compact
output, notably for LaTeX formatting, thanks to Marius Hofert.
The ‘utils::process.events()’ function has been added to trigger
immediate event handling.
‘Sys.which()’ now returns ‘NA’ (not ‘""’) for ‘NA’ inputs (related to
PR#15147).
The ‘print()’ method for class ‘"htest"’ gives fewer trailing spaces
(wish of PR#15124).
Also print output from ‘HoltWinters()’, ‘nls()’ and others.
‘loadNamespace()’ allows a version specification to be given, and this
is used to check version specifications given in the ‘Imports’ field
when a namespace is loaded.
‘setClass()’ has a new argument, ‘slots’, clearer and less ambiguous
than ‘representation’. It is recommended for future code, but should
be back-compatible. At the same time, the allowed slot specification
is slightly more general. See the documentation for details.
‘mget()’ now has a default for ‘envir’ (the frame from which it is
called), for consistency with ‘get()’ and ‘assign()’.
‘close()’ now returns an integer status where available, invisibly.
(Wish of PR#15088.)
The internal method of ‘tar()’ can now store paths too long for the
‘ustar’ format, using the (widely supported) GNU extension. It can
also store long link names, but these are much less widely supported.
There is support for larger files, up to the ‘ustar’ limit of 8GB.
Local reference classes have been added to package ‘methods’. These
are a technique for avoiding unneeded copying of large components of
objects while retaining standard R functional behavior. See
‘?LocalReferenceClasses’.
‘untar()’ has a new argument ‘restore_times’ which if false (not the
default) discards the times in the tarball. This is useful if they are
incorrect (some tarballs submitted to CRAN have times in a local time
zone or many years in the past even though the standard required them
to be in UTC).
‘replayplot()’ cannot (and will not attempt to) replay plots recorded
under R < 3.0.0. It may crash the R session if an attempt is made to
replay plots created in a different build of R >= 3.0.0.
Palette changes get recorded on the display list, so replaying plots
(including when resizing screen devices and using ‘dev.copy()’) will
work better when the palette is changed during a plot.
‘chol(pivot = TRUE)’ now defaults to LAPACK, not LINPACK.
The ‘parse()’ function has a new parameter ‘keep.source’, which
defaults to ‘options("keep.source")’.
Profiling _via_ ‘Rprof()’ now optionally records information at the
statement level, not just the function level.
The ‘Rprof()’ function now quotes function names in in its output file
on Windows, to be consistent with the quoting in Unix.
Profiling _via_ ‘Rprof()’ now optionally records information about time
spent in GC.
The HTML help page for a package now displays non-vignette
documentation files in a more accessible format.
To support ‘options(stringsAsFactors = FALSE)’, ‘model.frame()’,
‘model.matrix()’ and ‘replications()’ now automatically convert
character vectors to factors without a warning.
The ‘print’ method for objects of class ‘"table"’ now detects tables
with 0-extents and prints the results as, e.g., ‘< table of extent 0 x
1 x 2 >’. (Wish of PR#15198.)
Deparsing involving calls to anonymous functions has been made closer
to reversible by the addition of extra parentheses.
The function ‘utils::packageName()’ has been added as a lightweight
version of ‘methods::getPackageName()’.
‘find.package(lib.loc = NULL)’ now treats loaded namespaces
preferentially in the same way as attached packages have been for a
long time.
In Windows, the Change Directory dialog now defaults to the current
working directory, rather than to the last directory chosen in that
dialog.
‘available.packages()’ gains a ‘"license/restricts_use"’ filter which
retains only packages for which installation can proceed solely based
on packages which are guaranteed not to restrict use.
New ‘check_packages_in_dir()’ function in package ‘tools’ for
conveniently checking source packages along with their reverse
dependencies.
R's completion mechanism has been improved to handle help requests
(starting with a question mark). In particular, help prefixes are now
supported, as well as quoted help topics. To support this, completion
inside quotes are now handled by R by default on all platforms.
The memory manager now allows the strategy used to balance garbage
collection and memory growth to be controlled by setting the
environment variable ‘R_GC_MEM_GROW’. See ‘?Memory’ for more details.
(‘For experts only’, as the introductory manual says.) The use of
environment variables ‘R_NSIZE’ and ‘R_VSIZE’ to control the initial (=
minimum) garbage collection trigger for number of cons cels and size of
heap has been restored: they can be overridden by the command-line
options ‘--min-nsize’ and ‘--min-vsize’; see ‘?Memory’.
On Windows, the device name for bitmap devices as reported by ‘.Device’
and ‘.Devices’ no longer includes the file name. This is for
consistency with other platforms and was requested by the ‘lattice’
maintainer.
‘win.metafile()’ still uses the file name: the exact form is used by package ‘tkrplot’.
‘set.seed(NULL)’ re-initializes ‘.Random.seed’ as done at the beginning
of the session if not already set. (Suggestion of Bill Dunlap.)
The ‘breaks’ argument in ‘hist.default()’ can now be a function that
returns the breakpoints to be used (previously it could only return the
suggested number of breakpoints).
File ‘share/licenses/licenses.db’ has some clarifications, especially
as to which variants of ‘BSD’ and ‘MIT’ is intended and how to apply
them to packages. The problematic licence ‘Artistic-1.0’ has been
removed.
There is support for vectors longer than 2^31 - 1 elements. This
applies to raw, logical, integer, double, complex and character
vectors, as well as lists. (Elements of character vectors remain
limited to 2^31 - 1 bytes.)
Most operations which can sensibly be done with long vectors work:
others may return the error ‘long vectors not supported yet’. Most of
these are because they explicitly work with integer indices (e.g.,
‘anyDuplicated()’ and ‘match()’) or because other limits (e.g., of
character strings or matrix dimensions) would be exceeded or the
operations would be extremely slow.
‘length()’ returns a double for long vectors, and lengths can be set to
2^31 or more by the replacement function with a double value.
Most aspects of indexing are available. Generally double-valued
indices can be used to access elements beyond 2^31 - 1.
There is some support for matrices and arrays with each dimension less
than 2^31 but total number of elements more than that. Only some
aspects of matrix algebra work for such matrices, often taking a very
long time. In other cases the underlying Fortran code has an unstated
restriction (as was found for complex ‘svd()’).
‘dist()’ can produce dissimilarity objects for more than 65536 rows
(but for example ‘hclust()’ cannot process such objects).
‘serialize()’ to a raw vector is unlimited in size (except by
resources).
The C-level function ‘R_alloc’ can now allocate 2^35 or more bytes.
‘agrep()’ and ‘grep()’ will return double vectors of indices for long
vector inputs.
Many calls to ‘.C()’ have been replaced by ‘.Call()’ to allow long
vectors to be supported (now or in the future). Regrettably several
packages had copied the non-API ‘.C()’ calls and so failed.
‘.C()’ and ‘.Fortran()’ do not accept long vector inputs. This is a
precaution as it is very unlikely that existing code will have been
written to handle long vectors (and the R wrappers often assume that
‘length(x)’ is an integer).
Most of the methods for ‘sort()’ work for long vectors.
‘rank()’, ‘sort.list()’ and ‘order()’ support long vectors (slowly except for radix sorting).
‘sample()’ can do uniform sampling from a long vector.
More use has been made of R objects representing registered entry
points, which is more efficient as the address is provided by the
loader once only when the package is loaded.
This has been done for packages ‘base’, ‘methods’, ‘splines’ and ‘tcltk’: it was already in place for the other standard packages.
Since these entry points are always accessed by the R entry points they do not need to be in the load table which can be substantially smaller and hence searched faster. This does mean that ‘.C’ / ‘.Fortran’ / ‘.Call’ calls copied from earlier versions of R may no longer work - but they were never part of the API.
Many ‘.Call()’ calls in package ‘base’ have been migrated to
‘.Internal()’ calls.
‘solve()’ makes fewer copies, especially when ‘b’ is a vector rather
than a matrix.
‘eigen()’ makes fewer copies if the input has dimnames.
Most of the linear algebra functions make fewer copies when the
input(s) are not double (e.g., integer or logical).
A foreign function call (‘.C()’ etc) in a package without a ‘PACKAGE’
argument will only look in the first DLL specified in the ‘NAMESPACE’
file of the package rather than searching all loaded DLLs. A few
packages needed ‘PACKAGE’ arguments added.
The ‘@<-’ operator is now implemented as a primitive, which should
reduce some copying of objects when used. Note that the operator
object must now be in package ‘base’: do not try to import it
explicitly from package ‘methods’.
The transitional support for installing packages without namespaces
(required since R 2.14.0) has been removed. ‘R CMD build’ will still
add a namespace, but a ‘.First.lib()’ function will need to be
converted.
‘R CMD INSTALL’ no longer adds a namespace (so installation will fail), and a ‘.First.lib()’ function in a package will be ignored (with an installation warning for now).
As an exception, packages without a ‘R’ directory and no ‘NAMESPACE’ file can still be installed.
Packages can specify in their ‘DESCRIPTION file’ a line like
Biarch: yes
to be installed on Windows with ‘--force-biarch’.
Package vignettes can now be processed by other engines besides
‘Sweave’; see ‘Writing R Extensions’ and the ‘tools::vignetteEngine’
help topic for details.
The ‘*.R’ tangled source code for vignettes is now included in tarballs
when ‘R CMD build’ is used to produce them. In R 3.0.0, ‘*.R’ files
not in the sources will be produced at install time, but eventually
this will be dropped.
The package type ‘"mac.binary"’ now looks in a path in the repository
without any Mac subtype (which used to be ‘universal’ or ‘leopard’): it
looks in ‘bin/macosx/contrib/3.0’ rather than
‘bin/macosx/leopard/contrib/2.15’). This is the type used for the CRAN
binary distribution for OS X as from R 3.0.0.
File ‘etc/Makeconf’ makes more use of the macros ‘$(CC)’, ‘$(CXX)’,
‘$(F77)’ and ‘$(FC)’, so the compiler in use can be changed by setting
just these (and if necessary the corresponding flags and ‘FLIBS’) in
file ‘~/.R/Makevars’.
This is convenient for those working with binary distributions of R, e.g. on OS X.
‘R CMD check’ now gives a warning rather than a note if it finds calls
to ‘abort’, ‘assert’ or ‘exit’ in compiled code, and has been able to
find the ‘.o’ file in which the calls occur.
Such calls can terminate the R process which loads the package.
The location of the build and check environment files can now be
specified by the environment variables ‘R_BUILD_ENVIRON’ and
‘R_CHECK_ENVIRON’, respectively.
‘R CMD Sweave’ gains a ‘--compact’ option to control possibly reducing
the size of the PDF file it creates when ‘--pdf’ is given.
‘R CMD build’ now omits Eclipse's ‘.metadata’ directories, and ‘R CMD
check’ warns if it finds them.
‘R CMD check’ now does some checks on functions defined within
reference classes, including of ‘.Call()’ etc calls.
‘R CMD check --as-cran’ notes assignments to the global environment,
calls to ‘data()’ which load into the global environment, and calls to
‘attach()’.
‘R CMD build’ by default uses the internal method of ‘tar()’ to prepare
the tarball. This is more likely to produce a tarball compatible with
‘R CMD INSTALL’ and ‘R CMD check’: an external ‘tar’ program, including
options, can be specified _via_ the environment variable ‘R_BUILD_TAR’.
‘tools::massageExamples()’ is better protected against packages which
re-define base functions such as ‘cat()’ and ‘get()’ and so can cause
‘R CMD check’ to fail when checking examples.
‘R CMD javareconf’ has been enhanced to be more similar to the code
used by ‘configure’.
There is now a test that a JNI program can be compiled (like ‘configure’ did) and only working settings are used.
It makes use of custom settings from configuration recorded in ‘etc/javaconf’.
The ‘--no-vignettes’ argument of ‘R CMD build’ has been renamed to the
more accurate ‘--no-build-vignettes’: its action has always been to
(re)build vignettes and never omitted them.
‘R CMD check’ accepts ‘--no-build-vignettes’ as a preferred synonym for ‘--no-rebuild-vignettes’.
The ‘ENCODING’ argument to ‘.C()’ is defunct. Use ‘iconv()’ instead.
The ‘.Internal(eval.with.vis)’ non-API function has been removed.
Support for the converters for use with ‘.C()’ has been removed,
including the oft misused non-API header ‘R_ext/RConverters.h’.
The previously deprecated uses of ‘array()’ with a 0-length ‘dim’
argument and ‘tapply()’ with a 0-length ‘INDEX’ list are now errors.
‘Translation’ packages are defunct.
Calling ‘rep()’ or ‘rep.int()’ on a pairlist or other non-vector object
is now an error.
Several non-API entry points have been transferred to packages (e.g.,
‘R_zeroin2’) or replaced by different non-API entry points (e.g.,
‘R_tabulate’).
The ‘internal’ graphics device invoked by ‘.Call("R_GD_nullDevice",
package = "grDevices")’ has been removed: use ‘pdf(file = NULL)’
instead.
The ‘.Fortran()’ entry point ‘"dqrls"’ which has not been used by R
since version 2.15.1 is no longer available.
Functions ‘traceOn()’ and ‘traceOff()’ in package ‘methods’ are now
defunct.
Function ‘CRAN.packages()’ is finally defunct.
Use of ‘col2rgb(0)’ is defunct: use ‘par("bg")’ or ‘NA’ instead.
The long-defunct functions ‘Rd_parse()’, ‘anovalist.lm()’,
‘categpry()’, ‘clearNames()’, ‘gammaCody()’, ‘glm.fit.null()’,
‘lm.fit.null()’, ‘lm.wfit.null()’, ‘manglePackageNames()’,
‘mauchley.test()’, ‘package.contents()’, ‘print.coefmat()’,
‘reshapeLong()’, ‘reshapeWide()’, ‘tkclose()’, ‘tkcmd()’,
‘tkfile.dir()’, ‘tkfile.tail()’, ‘tkopen()’, ‘tkputs()’, ‘tkread()’,
‘trySilent()’ and ‘zip.file.extract()’ have been removed entirely (but
are still documented in the help system).
The unused ‘dataPath’ argument to ‘attachNamespace()’ has been removed.
‘grid.prompt()’ has been removed: use ‘devAskNewPage()’ instead.
The long-deprecated ‘intensities’ component is no longer returned by
‘hist()’.
‘mean()’ for data frames and ‘sd()’ for data frames and matrices are
defunct.
‘chol(pivot = FALSE, LINPACK = TRUE)’, ‘ch2inv(LINPACK = TRUE)’,
‘eigen(EISPACK = TRUE)’, ‘solve(LINPACK = TRUE)’ and ‘svd(LINPACK =
TRUE)’ are defunct: LAPACK will be used, with a warning.
The ‘keep.source’ argument to ‘library()’ and ‘require()’ is defunct.
This option needs to be set at install time.
Documentation for ‘real()’, ‘as.real()’ and ‘is.real()’ has been moved
to ‘defunct’ and the functions removed.
The ‘maxRasters’ argument of ‘pdf()’ (unused since R 2.14.0) has been
removed.
The unused ‘fontsmooth’ argument has been removed from the ‘quartz()’
device.
All the (non-API) EISPACK entry points in R have been removed.
‘chol(pivot = TRUE, LINPACK = TRUE)’ is deprecated.
The long-deprecated use of ‘\synopsis’ in the ‘Usage’ section of ‘.Rd’
files will be removed in R 3.1.0.
‘.find.package()’ and ‘.path.package()’ are deprecated: only the public
versions without the dot have ever been in the API.
In a package's ‘DESCRIPTION’ file,
License: X11
is deprecated, since it includes ‘Copyright (C) 1996 X Consortium’ which cannot be appropriate for a current R package. Use ‘MIT’ or ‘BSD_2_clause’ instead.
The C code underlying base graphics has been migrated to the ‘graphics’
package (and hence no longer uses ‘.Internal()’ calls).
Most of the ‘.Internal()’ calls used in the ‘stats’ package have been
migrated to C code in that package.
This means that a number of ‘.Internal()’ calls which have been used by packages no longer exist, including ‘.Internal(cor)’ ‘.Internal(cov)’, ‘.Internal(optimhess)’ and ‘.Internal(update.formula)’.
Some ‘.External()’ calls to the ‘base’ package (really to the R
executable or shared library) have been moved to more appropriate
packages. Packages should not have been using such calls, but some did
(mainly those used by ‘integrate()’).
There is a new function ‘mcaffinity()’ which allows getting or setting
the CPU affinity mask for the current R process on systems that
supports this (currently only Linux has been tested successfully). It
has no effect on systems which do not support process affinity. Users
are not expected to use this function directly (with the exception of
fixing libraries that break affinity settings like OpenBLAS) - the
function is rather intended to support affinity control in high-level
parallel functions. In the future, R may supplement lack of affinity
control in the OS by its own bookkeeping _via_ ‘mcaffinity()’ related
to processes and threads it spawns.
‘mcparallel()’ has a new argument ‘mc.affinity’ which attempts to set
the affinity of the child process according to the specification
contained therein.
The port used by socket clusters is chosen randomly: this should help
to avoid clashes observed when two users of a multi-user machine try to
create a cluster at the same time. To reproduce the previous behaviour
set environment variable ‘R_PARALLEL_PORT’ to ‘10187’.
There has been some minor re-organization of the non-API header files.
In particular, ‘Rinternals.h’ no longer includes the non-API header
‘R_exts/PrtUtil.h’, and that no longer includes ‘R_exts/Print.h’.
Passing ‘NULL’ to ‘.C()’ is now an error.
‘.C()’ and ‘.Fortran()’ now warn if ‘"single"’ arguments are used with
‘DUP = FALSE’, as changes to such arguments are not returned to the
caller.
C entry points ‘R_qsort’ and ‘R_qsort_I’ now have ‘start’ and ‘end’ as
‘size_t’ to allow them to work with longer vectors on 64-bit platforms.
Code using them should be recompiled.
A few recently added C entry points were missing the remapping to
‘Rf_’, notably ‘[dpq]nbinom_mu’.
Some of the interface pointers formerly available only to ‘R.app’ are
now available to front-ends on all Unix-alikes: one has been added for
the interface to ‘View()’.
‘PACKAGE = ""’ is now an error in ‘.C()’ etc calls: it was always
contrary to the documentation.
Entry point ‘rcont2’ has been migrated to package ‘stats’ and so is no
longer available.
‘R_SVN_REVISION’ in ‘Rversion.h’ is now an integer (rather than a
string) and hence usable as e.g. ‘#if R_SVN_REVISION < 70000’.
The entry points ‘rgb2hsv’ and ‘hsv2rgb’ have been migrated to package
‘grDevices’ and so are no longer available.
‘R_GE_version’ has been increased to ‘10’ and ‘name2col’ removed (use
‘R_GE_str2col’ instead). R internal colour codes are now defined using
the typedef ‘rcolor’.
The ‘REPROTECT’ macro now checks that the protect index is valid.
Several non-API entry points no longer used by R have been removed,
including the Fortran entry points ‘chol’, ‘chol2inv’, ‘cg’, ‘ch’ and
‘rg’, and the C entry points ‘Brent_fmin’, ‘fft_factor’ and ‘fft_work’.
If a ‘.External’ call is registered with a number of arguments (other
than ‘-1’), the number of arguments passed is checked for each call (as
for other foreign function calls).
It is now possible to write custom connection implementations outside
core R using ‘R_ext/Connections.h’. Please note that the
implementation of connections is still considered internal and may
change in the future (see the above file for details).
The management of translations has been converted to R code: see
‘?tools::update_pkg_po’.
The translations for the R interpreter and ‘RGui.exe’ are now part of
the ‘base’ package (rather than having sources in directory ‘po’ and
being installed to ‘share/locale’). Thus the ‘base’ package supports
three translation domains, ‘R-base’, ‘R’ and ‘RGui’.
The compiled translations which ship with R are all installed to the
new package ‘translations’ for easier updating. The first package of
that name found on ‘.libPaths()’ at the start of the R session will be
used. (It is possible messages will be used before ‘.libPaths()’ is
set up in which case the default translations will be used: set
environment variable ‘R_TRANSLATIONS’ to point to the location of the
intended ‘translations’ package to use this right from the start.)
The translations form a separate group in the Windows installer, so can
be omitted if desired.
The markup for many messages has been changed to make them easier to
translate, incorporating suggestions from Łukasz Daniel.
There is again support for building without using the C ‘long double’
type. This is required by C99, but system implementations can be slow
or flawed. Use ‘configure’ option ‘--disable-long-double’.
‘make pdf’ and ‘make install-pdf’ now make and install the full
reference index (including all base and recommended packages).
The 'reference manual' on the Windows GUI menu and included in the
installer is now the full reference index, including all base and
recommended packages.
R help pages and manuals have no ISBNs because ISBN rules no longer
allow constantly changing content to be assigned an ISBN.
The Windows installer no longer installs a Start Menu link to the
static help pages; as most pages are generated dynamically, this led to
a lot of broken links.
Any custom settings for Java configuration are recorded in file
‘etc/javaconf’ for subsequent use by ‘R CMD javareconf’.
There is now support for ‘makeinfo’ version 5.0 (which requires a
slightly different ‘.texi’ syntax).
The minimum versions for ‘--use-system-zlib’ and ‘--use-system-pcre’
are now tested as 1.2.5 and 8.10 respectively.
On Windows, the stack size is reduced to 16MB on 32-bit systems:
misguided users were launching many threads without controlling the
stack size.
‘configure’ no longer looks for file ‘~/.Rconfig’: ‘~/.R/config’ has
long been preferred.
When ‘R CMD build’ is run in an encoding other than the one specified
in the package's ‘DESCRIPTION’ file it tries harder to expand the
‘authors@R’ field in the specified encoding. (PR#14958)
If ‘R CMD INSTALL’ is required to expand the ‘authors@R’ field of the
‘DESCRIPTION’ file, it tries harder to do so in the encoding specified
for the package (rather than using ASCII escapes).
Fix in package ‘grid’ for pushing a viewport into a layout cell, where
the layout is within a viewport that has zero physical width OR where
the layout has zero total relative width (likewise for height). The
layout column widths (or row heights) in this case were being
calculated with non-finite values. (Reported by Winston Chang.)
‘solve(A, b)’ for a vector ‘b’ gave the answer names from ‘colnames(A)’
for ‘LINPACK = TRUE’ but not in the default case.
‘La.svd()’ accepts logical matrices (as documented, and as ‘svd()’
did).
‘legend()’ now accepts negative ‘pch’ values, in the same way
‘points()’ long has.
Parse errors when installing files now correctly display the name of
the file containing the bad code.
In Windows, tcltk windows were not always properly constructed.
(PR#15150)
The internal functions implementing ‘parse()’, ‘tools::parseLatex()’
and ‘tools::parse_Rd()’ were not reentrant, leading to errors in rare
circumstances such as a garbage collection triggering a recursive call.
Field assignments in reference class objects _via_ ‘$<-’ were not being
checked because the magic incantation to turn methods on for that
primitive operator had been inadvertently omitted.
‘setHook(hookname, value, action="replace")’ set the hook to be the
value, rather than a list containing the value as documented.
(PR#15167)
If a package used a ‘NEWS.Rd’ file, the main HTML package index page
did not link to it. (Reported by Dirk Eddelbuettel.)
The primitive implementation of ‘@<-’ was not checking the class of the
replacement. It now does a check, quicker but less general than
‘slot<-’. See the help.
‘split(x, f)’ now recycles classed objects ‘x’ in the same way as
vectors. (Reported by Martin Morgan.)
‘pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE)’ is no longer
‘-Inf’; ditto for corresponding ‘pt()’ and ‘pf()’ calls, such as
‘pt(45, df=5000, lower.tail=FALSE, log.p=TRUE)’. (PR#15162)
The Windows graphics device would crash R if a user attempted to load
the graphics history from a variable that was not a saved history.
(PR#15230)
The workspace size for the ‘predict()’ method for ‘loess()’ could
exceed the maximum integer size. (Reported by Hiroyuki Kawakatsu.)
‘ftable(x, row.vars, col.vars)’ now also works when the ‘*.vars’
arguments are (integer or character vectors) of length zero.
Calling ‘cat()’ on a malformed UTF-8 string could cause the Windows GUI
to lock up. (PR#15227)
‘removeClass(cc)’ gave "node stack overflow" for some class definitions
containing ‘"array"’ or ‘"matrix"’.
‘matrix’ objects now also inherit from class ‘"array"’, namely, e.g., ‘class(diag(1))’ is ‘c("matrix", "array")’ which invalidates code assuming that ‘length(class(obj)) == 1’, an incorrect assumption that is less frequently fulfilled now.
S3 methods for ‘"array"’, i.e., ‘<someFun>.array()’, are now also dispatched for ‘matrix’ objects.
R now provides a syntax for specifying raw character constants similar to the one used in C++: ‘r"(...)"’ with ‘...’ any character sequence, except that it must not contain the closing sequence ‘)"’. This makes it easier to write strings that contain backslashes or both single and double quotes. For more details see ‘?Quotes’.
‘N <- NULL; N[[1]] <- val’ now turns ‘N’ into a ‘list’ also when ‘length(val) == 1’, for consistency. This enables ‘dimnames(r1)[[1]] <- "R1"’ for a 1-row matrix ‘r1’, fixing PR#17719, reported by Serguei Sokol.
‘deparse(..)’, ‘dump(..)’, and ‘dput(x, control="all")’ now include using control option ‘"digits17"’ which typically ensures 1:1 invertibility. New option ‘control = "exact"’ ensures numeric exact invertibility via ‘"hexDigits"’.
R now uses a ‘stringsAsFactors = FALSE’ default, and hence by default no longer converts strings to factors in calls to ‘data.frame()’ and ‘read.table()’.
When loading data sets via ‘read.table()’, ‘data()’ now uses ‘LC_COLLATE=C’ to ensure locale independent results for possible string-to-factor conversions.
The ‘plot()’ S3 generic function is now in package ‘base’ rather than package ‘graphics’, as it is reasonable to have methods that do not use the ‘graphics’ package. The generic is currently re-exported from the ‘graphics’ namespace to allow packages importing it from there to continue working, but this may change in future versions of R.
Packages which define S4 generics for ‘plot()’ should be re-installed and package code using such generics from other packages needs to ensure that they are imported rather than rely on their being found on the search path (as in a namespace, the base namespace has priority over the search path).
R now uses reference counting instead of the ‘NAMED’ mechanism for determining when objects can be safely mutated in base C code. This reduces the need for copying in some cases and should allow further optimizations in the future. It should also help make the internal code easier to maintain. This change is expected to have minimal impact on packages not using unsupported coding practices in their C/C++ code.
R is now built against a PCRE2 library for Perl-like regular expressions. (On non-Windows platforms PCRE1 can optionally be used if PCRE2 is not available at build time.) The version of PCRE in use can be obtained via ‘extSoftVersion()’: PCRE1 has versions < 10, PCRE2 versions >= 10.
PCRE2 reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used with PCRE2, and is reported as ‘FALSE’ when that is in use.
Making PCRE2 available when building R from source is strongly recommended (preferably version 10.30 or later) as PCRE1 is no longer developed (it only receives bug fixes and has outdated Unicode tables)
‘assertError()’ and ‘assertWarning()’ (in package ‘tools’) can now check for _specific_ error or warning classes _via_ the new optional second argument ‘classes’ (which is not back compatible with previous use of an unnamed second argument).
‘DF2formula()’, the utility for the data frame method of ‘formula()’, now works without parsing and explicit evaluation, starting from Suharto Anggono's suggestion in PR#17555.
‘approxfun()’ and ‘approx()’ gain a new argument ‘na.rm’ defaulting to true. If set to false, missing ‘y’ values now propagate into the interpolated values.
Long vectors are now supported as the ‘seq’ argument of a ‘for()’ loop.
‘str(x)’ gets a new ‘deparse.lines’ option with a default to speed it up when ‘x’ is a large ‘call’ object.
The internal traceback object produced when an error is signalled (‘.Traceback’), now contains the ‘call’s rather than the _‘deparse()’d_ calls, deferring the deparsing to the user-level functions ‘.traceback()’ and ‘traceback()’, fulfilling the wish of PR#17580, reported incl. two patch proposals by Brodie Gaslam.
‘data.matrix()’ now converts character columns to factors and from this to integers.
‘package.skeleton()’ now explicitly lists all exports in the ‘NAMESPACE’ file.
New function ‘.S3method()’ to register S3 methods in R scripts.
‘file.path()’ has some support for file paths not in the session encoding, e.g. with UTF-8 inputs in a non-UTF-8 locale the output is marked as UTF-8.
Most functions with file-path inputs will give an explicit error if a file-path input in a marked encoding cannot be translated (to the native encoding or in some cases on Windows to UTF-8), rather than translate to a different file path using escapes. Some (such as ‘dir.exists()’, ‘file.exists()’, ‘file.access()’, ‘file.info()’, ‘list.files()’, ‘normalizePath()’ and ‘path.expand()’) treat this like any other non-existent file, often with a warning.
New function ‘list2DF()’ for creating data frames from lists of variables.
‘iconv()’ has a new option ‘sub = "Unicode"’ to translate UTF-8 input invalid in the ‘to’ encoding using ‘<U+xxxx>’ escapes.
There is a new help document accessed by ‘help("file path encoding")’ detailing how file paths with marked encodings are handled.
There is a new function ‘infoRDS()’ providing information about the serialization format of a serialized object.
S3 method lookup now by default skips the elements of the search path between the global and base environments.
Added an argument ‘add_datalist(*, small.size = 0)’ to allow the creation of a ‘data/datalist’ file even when the total size of the data sets is small.
The backquote function ‘bquote()’ has a new argument ‘splice’ to enable splicing a computed list of values into an expression, like ‘,@’ in LISP's backquote.
The formula interface to ‘t.test()’ and ‘wilcox.test()’ has been extended to handle one-sample and paired tests.
The ‘palette()’ function has a new default set of colours (which are less saturated and have better accessibility properties). There are also some new built-in palettes, which are listed by the new ‘palette.pals()’ function. These include the old default palette under the name ‘"R3"’. Finally, the new ‘palette.colors()’ function allows a subset of colours to be selected from any of the built-in palettes.
‘n2mfrow()’ gains an option ‘asp = 1’ to specify the aspect ratio, fulfilling the wish and extending the proposal of Michael Chirico in PR#17648.
‘head(x, n)’ and ‘tail()’ default and other S3 methods notably for _vector_ ‘n’, e.g. to get a “corner” of a matrix, also extended for ‘array’'s of higher dimension, thanks to the patch proposal by Gabe Becker in PR#17652. Consequently, optional argument ‘addrownums’ is deprecated and replaced by the (more general) ‘keepnums’. Invalid (second argument) ‘n’ now leads to typically more easily readable error messages.
New function ‘.class2()’ provides the full character vector of class names used for S3 method dispatch.
Printing ‘methods(..)’ now uses new ‘format()’ method.
‘sort.list(x)’ now works for non-atomic objects ‘x’ and ‘method="auto"’ (default) or ‘"radix"’ in cases ‘order(x)’ works.
Where available, ‘writeBin()’ now allows long vectors (those of length >= 2^31).
New function ‘deparse1()’ produces one string, wrapping ‘deparse()’, to be used typically in ‘deparse1(substitute(*))’, e.g., to fix PR#17671.
‘wilcox.test()’ enhancements: In the (non-paired) two-sample case, ‘Inf’ values are treated as very large for robustness consistency. If exact computations are used, the result now has ‘"exact"’ in the ‘method’ element of its return value. New arguments ‘tol.root’ and ‘digits.rank’. The latter may be used for stability to treat very close numbers as ties.
‘readBin()’ and ‘writeBin()’ now report an error for invalid ‘endian’ value. The affected code needs to be fixed with care as the old undocumented behavior was to swap endian-ness in such cases.
‘sequence()’ is now an S3 generic, with an internally implemented default method, and gains arguments to generate more complex sequences. Based on code from the ‘S4Vectors’ Bioconductor package and the advice of Hervé Pagès.
‘print()’'s default method and many other methods (by calling the default eventually and passing ‘...’) now make use of a new optional ‘width’ argument, avoiding the need for the user to set and reset ‘options("width")’.
‘memDecompress()’ supports the RFC 1952 format (e.g. in-memory copies of ‘gzip’-compressed files) as well as RFC 1950.
‘memCompress()’ and ‘memDecompress()’ support long raw vectors for types ‘"gzip"’ and ‘"zx"’.
‘sweep()’ and ‘slice.index()’ can now use names of dimnames for their ‘MARGIN’ argument (‘apply’ has had this for almost a decade).
New function ‘proportions()’ and ‘marginSums()’. These should replace the unfortunately named ‘prop.table()’ and ‘margin.table()’. They are drop-in replacements, but also add named-margin functionality. The old function names are retained as aliases for back-compatibility.
Functions ‘rbinom()’, ‘rgeom()’, ‘rhyper()’, ‘rpois()’, ‘rnbinom(),’ ‘rsignrank()’ and ‘rwilcox()’ which have returned integer since R 3.0.0 and hence ‘NA’ when the numbers would have been outside the integer range, now return double vectors (without NAs, typically) in these cases.
‘matplot(x,y)’ (and hence ‘matlines()’ and ‘matpoints()’) now call the corresponding methods of ‘plot()’ and ‘lines()’, e.g, when ‘x’ is a ‘"Date"’ or ‘"POSIXct"’ object; prompted by Spencer Graves' suggestion.
‘stopifnot()’ now allows customizing error messages via argument names, thanks to a patch proposal by Neal Fultz in PR#17688.
‘unlink()’ gains a new argument ‘expand’ to disable wildcard and tilde expansion.
‘mle()’ in the ‘stats4’ package has had its interface extended so that arguments to the negative log-likelihood function can be one or more vectors, with similar conventions applying to bounds, start values, and parameter values to be kept fixed. This required a minor extension to class ‘"mle"’, so saved objects from earlier versions may need to be recomputed.
The default for ‘pdf()’ is now ‘useDingbats = FALSE’.
The default (fill colour) for both ‘hist()’ and ‘boxplot()’ is now ‘col = "lightgray"’.
The default order of the levels on the y-axis for both ‘spineplot()’ and ‘cdplot()’ has been reversed.
If the ‘R_ALWAYS_INSTALL_TESTS’ environment variable is set to a true value, ‘R CMD INSTALL’ behaves as if the ‘--install-tests’ option is always specified. Thanks to Reinhold Koch for the suggestion.
New function ‘R_user_dir()’ in package ‘tools’ for paths appropriate for storing R-related user-specific data, configuration and cache files.
‘capabilities()’ gains a new logical option ‘Xchk’ to avoid warnings about X11-related capabilities.
The internal implementation of ‘grid’ units has changed, but the only visible effects at user-level should be: a slightly different print format for some units (especially unit arithmetic); faster performance (for unit operations); and two new functions ‘unitType()’ and ‘unit.psum()’. Based on code contributed by Thomas Lin Pedersen.
When internal dispatch for ‘rep.int()’ and ‘rep_len()’ fails, there is an attempt to dispatch on the equivalent call to ‘rep()’.
Object ‘.Machine’ now contains new ‘longdouble.*’ entries (when R uses long doubles internally).
‘Rterm’ now works also when invoked from MSYS2 terminals. Line editing is possible when command ‘winpty’ is installed.
‘normalizePath()’ now resolves symbolic links and normalizes case of long names of path elements in case-insensitive folders (PR#17165).
‘md5sum()’ supports UTF-8 file names with characters that cannot be translated to the native encoding (PR#17633).
‘Rterm’ gains a new option ‘--workspace’ to specify the workspace to be restored. This allows equals to be part of the name when opening via Windows file associations (reported by Christian Asseburg).
‘Rterm’ now accepts ‘ALT+xxx’ sequences also with NumLock on. Tilde can be pasted with an Italian keyboard (PR#17679).
Make macro ‘F77_VISIBILITY’ has been removed and replaced by ‘F_VISIBILITY’.
Make macros ‘F77’, ‘FCPIFCPLAGS’ and ‘SHLIB_OPENMP_FCFLAGS’ have been removed and replaced by ‘FC’, ‘FPICFLAGS’ and ‘SHLIB_OPENMP_FFLAGS’ respectively. (Most ‘make’ programs will set ‘F77’ to the value of ‘FC’, which is set for package compilation. But portable code should not rely on this.)
The deprecated support for specifying C++98 for package installation has been removed.
‘R CMD config’ no longer knows about the unused settings ‘F77’ and ‘FCPIFCPLAGS’, nor ‘CXX98’ and similar.
Either PCRE >= 8.32 (Nov 2012) or PCRE2 is required: the deprecated provision for 8.20-8.31 has been removed.
‘installChar’ is now remapped in ‘Rinternals.h’ to ‘installTrChar’, of which it has been a wrapper since R 3.6.0. Neither are part of the API, but packages using ‘installChar’ can replace it if they depend on ‘R >= 3.6.2’.
Header ‘R_ext/Print.h’ defines ‘R_USE_C99_IN_CXX’ and hence exposes ‘Rvprintf’ and ‘REvprintf’ if used with a C++11 (or later) compiler.
There are new Fortran subroutines ‘dblepr1’, ‘realpr1’ and ‘intpr1’ to print a scalar variable (‘gfortran’ 10 enforces the distinction between scalars and length-one arrays). Also ‘labelpr’ to print just a label.
User-set ‘DEFS’ (e.g., in ‘config.site’) is now used for compiling packages (including base packages).
There is a new variant option ‘--enable-lto=check’ for checking consistency of BLAS/LAPACK/LINPACK calls - see ‘Writing R Extensions’.
A C++ compiler default is set only if the C++11 standard is supported: it no longer falls back to C++98.
PCRE2 is used if available. To make use of PCRE1 if PCRE2 is unavailable, configure with option ‘--with-pcre1’.
The minimum required version of ‘libcurl’ is now 7.28.0 (Oct 2012).
‘R --help’ now mentions the option ‘--no-echo’ (renamed from ‘--slave’) and its previously undocumented short form ‘-s’.
‘R CMD check’ now optionally checks ‘configure’ and ‘cleanup’ scripts for non-Bourne-shell code (‘bashisms’).
‘formula(x)’ with ‘length(x) > 1’ character vectors, is deprecated now. Such use has been rare, and has ‘worked’ as expected in some cases only. In other cases, wrong ‘x’ have silently been truncated, not detecting previous errors.
Long-standing issue where the X11 device could lose events shortly after startup has been addressed (PR#16702).
The ‘data.frame’ method for ‘rbind()’ no longer drops ‘<NA>’ levels from factor columns by default (PR#17562).
‘available.packages()’ and hence ‘install.packages()’ now pass their ‘...’ argument to ‘download.file()’, fulfilling the wish of PR#17532; subsequently, ‘available.packages()’ gets new argument ‘quiet’, solving PR#17573.
‘stopifnot()’ gets new argument ‘exprObject’ to allow an R object of class ‘expression’ (or other ‘language’) to work more consistently, thanks to suggestions by Suharto Anggono.
‘conformMethod()’ now works correctly in cases containing a “‘&&’ logic” bug, reported by Henrik Bengtsson. It now creates methods with ‘"missing"’ entries in the signature. Consequently, ‘rematchDefinition()’ is amended to use appropriate ‘.local()’ calls with named arguments where needed.
‘format.default(*, scientific = FALSE)’ now corresponds to a practically most extreme ‘options(scipen = n)’ setting rather than arbitrary ‘n = 100’.
‘format(as.symbol("foo"))’ now works (returning ‘"foo"’).
‘postscript(.., title = *)’ now signals an error when the title string contains a character which produces corrupt PostScript, thanks to Daisuko Ogawa's PR#17607.
Certain ‘Ops’ (notably comparison such as ‘==’) now also work for 0-length data frames, after reports by Hilmar Berger.
‘methods(class = class(glm(..)))’ now warns more usefully and only once.
‘write.dcf()’ no longer mangles field names (PR#17589).
‘Sys.glob()’ on Windows now supports all characters from the Unicode Basic Multilingual Plane, no longer corrupting (less commonly used) characters (PR#17638).
Primitive replacement functions no longer mutate a referenced first argument when used outside of a complex assignment context.
Better error message for ‘contour(*, levels = Inf)’.
The return value of ‘contourLines()’ is no longer ‘invisible()’.
(Windows) ‘Rterm’ now correctly displays multi-byte-coded characters representable in the current native encoding (at least on Windows 10 they were sometimes omitted, PR#17632).
The Fortran code for calculating the ‘coefficients’ component in ‘lm.influence()’ was very inefficient. It has (for now) been replaced with much faster R code (PR#17624).
‘cm.colors(n)’ _etc_ no longer append the code for ‘alpha = 1’, ‘"FF"’, to all colors. Hence all eight ‘*.colors()’ functions and ‘rainbow()’ behave consistently and have the same non-explicit default (PR#17659).
‘dnorm’ had a problematic corner case with ‘sd == -Inf’ and negative ‘sd’ which was not flagged as an error in all cases. Thanks to Stephen D. Weigand for reporting and Wang Jiefei for analyzing this; similar change has been made in ‘dlnorm()’.
The optional ‘iter.smooth’ argument of ‘plot.lm()’, (the ‘plot()’ method for ‘lm’ and ‘glm’ fits) now defaults to ‘0’ for all ‘glm’ fits. Especially for binary observations with high or low fitted probabilities, this effectively deleted all observations of 1 or 0. Also, the type of residuals used in the ‘glm’ case has been switched to ‘"pearson"’ since deviance residuals do not in general have approximately zero mean.
In ‘plot.lm’, Cook's distance was computed from unweighted residuals, leading to inconsistencies. Replaced with usual weighted version. (PR#16056)
Time-series ‘ts(*, start, end, frequency)’ with fractional ‘frequency’ are supported more consistently; thanks to a report from Johann Kleinbub and analysis and patch by Duncan Murdoch in PR#17669.
In case of errors ‘mcmapply()’ now preserves attributes of returned ‘"try-error"’ objects and avoids simplification, overriding ‘SIMPLIFY’ to ‘FALSE’. (PR#17653)
‘as.difftime()’ gets new optional ‘tz = "UTC"’ argument which should fix behaviour during daylight-savings-changeover days, fixing PR#16764, thanks to proposals and analysis by Johannes Ranke and Kirill Müller.
‘round()’ does a better job of rounding _“to nearest”_ by _measuring_ and _“to even”_; thanks to a careful algorithm originally prompted by the report from Adam Wheeler and then others, in PR#17668. ‘round(x, dig)’ for _negative_ digits is much more rational now, notably for large |dig|.
Inheritance information on S4 classes is maintained more consistently, particularly in the case of class unions (in part due to PR#17596 and a report from Ezra Tucker).
‘is()’ behaves more robustly when its argument ‘class2’ is a ‘classRepresentation’ object.
The warning message when attempting to export an nonexistent class is now more readable; thanks to Thierry Onkelinx for recognizing the problem.
‘scan()’ issues with UTF-8 data when running in a DBCS locale (on Windows) have been resolved (PR#16520,PR#16584).
‘choose()’ misbehaved in corner cases where it switched ‘n - k’ for ‘k’ and ‘n’ was only _nearly_ integer (report from Erik Scott Wright).
‘mle()’ in the ‘stats4’ package had problems combining use of box constraints and fixed starting values (in particular, confidence intervals were affected).
Operator ‘?’ now has lower precedence than ‘=’ to work as documented and to behave like ‘<-’ in help expressions (PR#16710).
‘smoothEnds(x)’ now returns ‘integer’ type in _both_ cases when ‘x’ is ‘integer’, thanks to report and proposal by Bill Dunlap PR#17693.
The ‘methods’ package does a better job of tracking inheritance relationships across packages.
‘norm(diag(c(1, NA)), "2")’ now works.
‘subset()’ had problems with 0-col dataframes (Bill Dunlap, PR#17721)
Several cases of integer overflow detected by the ‘undefined behaviour analyser’ of ‘clang’ 10 have been circumvented. One in ‘rhyper()’ may change the generated value for large input values.
‘dotchart()’ now places the y-axis label (‘ylab’) much better, not overplotting labels, thanks to a report and suggestion by Alexey Shipunov.
‘head(x, n)’ and ‘tail()’ default and other S3 methods notably for _vector_ ‘n’, e.g. to get a “corner” of a matrix, also extended for ‘array’'s of higher dimension, thanks to the patch proposal by Gabe Becker in PR#17652. Consequently, optional argument ‘addrownums’ is deprecated and replaced by the (more general) ‘keepnums’. Invalid (second argument) ‘n’ now leads to typically more easily readable error messages.
Where available, ‘writeBin()’ now allows long vectors (those of length >= 2^31).
‘wilcox.test()’ enhancements: In the (non-paired) two-sample case, ‘Inf’ values are treated as very large for robustness consistency. If exact computations are used, the result now has ‘"exact"’ in the ‘method’ element of its return value. New arguments ‘tol.root’ and ‘digits.rank’. The latter may be used for stability to treat very close numbers as ties.
New function ‘proportions()’ and ‘marginSums()’. These should replace the unfortunately named ‘prop.table()’ and ‘margin.table()’. They are drop-in replacements, but also add named-margin functionality. The old function names are retained as aliases for back-compatibility.
‘mle()’ in the ‘stats4’ package has had its interface extended so that arguments to the negative log-likelihood function can be one or more vectors, with similar conventions applying to bounds, start values, and parameter values to be kept fixed. This required a minor extension to class ‘"mle"’, so saved objects from earlier versions may need to be recomputed.
The internal implementation of ‘grid’ units has changed, but the only visible effects at user-level should be: a slightly different print format for some units (especially unit arithmetic); faster performance (for unit operations); and two new functions ‘unitType()’ and ‘unit.psum()’. Based on code contributed by Thomas Lin Pedersen.
‘Rterm’ now accepts ‘ALT+xxx’ sequences also with NumLock on. Tilde can be pasted with Italian keyboard (PR#17679).
Header ‘R_ext/Print.h’ defines ‘R_USE_C99_IN_CXX’ and hence exposes ‘Rvprintf’ and ‘REprintf’ if used with a C++11 (or later) compiler.
‘R CMD check --as-cran’ now uses a ‘stringsAsFactors = FALSE’ default
setting.
‘dotchart()’ now places the y-axis label (‘ylab’) much better, not overplotting labels, thanks to a report and suggestion by Alexey Shipunov.
‘Sys.glob()’ on Windows now supports all characters from the Unicode Basic Multilingual Plane, no longer corrupting (less commonly used) characters (PR#17638).
The return value of ‘contourLines()’ is no longer ‘invisible()’.
The Fortran code for calculating the ‘coefficients’ component in ‘lm.influence()’ was very inefficient. It has (for now) been replaced with much faster R code (PR#17624).
‘cm.colors(n)’ _etc_ no longer append the code for ‘alpha = 1’, ‘"FF"’, to all colors. Hence all eight ‘*.colors()’ functions and ‘rainbow()’ behave consistently and have the same non-explicit default (PR#17659).
‘dnorm’ had a problematic corner case with ‘sd == -Inf’ and negative ‘sd’ which was not flagged as error in all cases. Thanks to Stephen D. Weigand for reporting and Wang Jiefei for analyzing this; similar change has been made in ‘dlnorm()’.
The optional ‘iter.smooth’ argument of ‘plot.lm()’, (the ‘plot()’ method for ‘lm’ and ‘glm’ fits) now defaults to ‘0’ for all ‘glm’ fits. Especially for binary observations with high or low fitted probabilities, this effectively deleted all observations of 1 or 0, respectively. Also, the type of residuals used in the ‘glm’ case has been switched to ‘"pearson"’ since deviance residuals do not in general have approximately zero mean.
In case of errors ‘mcmapply()’ now preserves attributes of returned ‘"try-error"’ objects and avoids simplification, overriding ‘SIMPLIFY’ to ‘FALSE’. (PR#17653)
‘as.difftime()’ gets new optional ‘tz = "UTC"’ argument which should fix behaviour during daylight-savings-changeover days, fixing PR#16764, thanks to proposals and analysis by Johannes Ranke and Kirill Müller.
‘is()’ behaves more robustly when its argument ‘class2’ is a ‘classRepresentation’ object.
R is now built by default against a PCRE2 library for Perl-like regular expressions. On non-Windows platforms PCRE1 is used if PCRE2 is not available at build.time. The version of PCRE used can be obtained via ‘extSoftVersion()’: PCRE1 has versions < 10, PCRE2 versions >= 10.
PCRE2 is stricter in some cases and reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used, and reported as ‘FALSE’.
The ‘plot()’ S3 generic function is now in package ‘base’ rather than package ‘graphics’, as it is reasonable to have methods that do not use the ‘graphics’ package. The generic is currently re-exported from the ‘graphics’ namespace to allow packages importing it from there to continue working, but this may change in future versions of R.
Packages which define S4 generics for ‘plot()’ should be re-installed and package code using such generics from other packages needs to ensure that they are imported rather than rely on their being found on the search path (as in a namespace, the base namespace has priority over the search path).
‘.Machine’ now contains new ‘longdouble.*’ entries (when R internally uses long double).
‘subset()’ had problems with 0-col dataframes (Bill Dunlap, PR#17721)
The ‘plot()’ generic function is now in package ‘base’ rather than package ‘graphics’, as it is reasonable to have methods that do not use the ‘graphics’ package. The generic is currently re-exported from the ‘graphics’ namespace to allow packages importing it from there to continue working, but this may change in future versions of R.
R now builds by default against a PCRE2 library for Perl-like regular expressions if available at build time on non-Windows platforms (otherwise PCRE1 is used as in older versions of R). On Windows, R always builds against PCRE2 by default.
PCRE2 is stricter in some cases and reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used, and reported as ‘FALSE’.
The version of PCRE used can be obtained via ‘extSoftVersion()’, PCRE1 has versions < 10, PCRE2 versions >= 10.
When internal dispatch for ‘rep.int()’ and ‘rep_len()’ fails, there is an attempt to dispatch on the equivalent call to ‘rep()’.
‘deparse(..)’, ‘dump(..)’, and ‘dput(x, control="all")’ now include using control option ‘"digits17"’ which typically ensures 1:1 invertibility. New option ‘control = "exact"’ ensures numeric exact invertibility via ‘"hexDigits"’.
R now uses a ‘stringsAsFactors = FALSE’ default, and hence by default no longer converts strings to factors in calls to ‘data.frame()’ and ‘read.table()’.
When loading data sets via ‘read.table()’, ‘data()’ now uses ‘LC_COLLATE=C’ to ensure locale independent results for possible string to factor conversions.
‘capabilities()’ gains a new logical option ‘Xchk’ to avoid warnings about X11-related capabilities.
The internal implementation of ‘grid’ units has changed, but the only visible effect at user-level should be: a slightly different print format for some units (especially unit arithmetic); faster performance (for unit operations); and two new functions ‘unitType()’ and ‘unit.psum()’. Original code contributed by Thomas Lin Pedersen.
Several cases of integer overflow detected by the ‘undefined behaviour analyser’ of clang 10 have been circumvented. One in ‘rhyper()’ may change the generated value for large input values.
New function ‘R_user_dir()’ in package ‘tools’ for paths appropriate for storing R-related user-specific data, configuration and cache files.
If the ‘R_ALWAYS_INSTALL_TESTS’ environment variable is set to a true value, ‘R CMD INSTALL’ behaves as if the ‘--install-tests’ option is always specified. Thanks to Reinhold Koch for the suggestion.
‘R CMD check --as-cran’ now uses a ‘stringsAsFactors = FALSE’ default setting.
‘subset()’ had problems with 0-col dataframe (Bill Dunlap, PR#17721)
The default for ‘pdf()’ is now ‘useDingbats = FALSE’.
The default (fill colour) for both ‘hist()’ and ‘boxplot()’ is now ‘col = "lightgray"’.
The default order of the levels on the y-axis for both ‘spineplot()’ and ‘cdplot()’ has been reversed.
‘N <- NULL; N[[1]] <- val’ now turns ‘N’ into a ‘list’ also when ‘length(val) == 1’, consistently. This also enables ‘dimnames(r1)[[1]] <- "R1"’ for a 1-row matrix ‘r1’, fixing PR#17719, reported by Serguei Sokol.
There are new Fortran subroutines ‘dblepr1’, ‘realpr1’ and ‘intpr1’ to print a scalar variable (‘gfortran’ 10 enforces the distinction between scalars and length-one arrays). Also ‘labelpr’ to print just a label.
The included LAPACK has been updated to version 3.9.0 (for the included routines, just bug fixes).
Fixed a C level integer overflow in ‘rhyper()’; reported by Benjamin Tyner in PR#17694.
Uses of ‘url(gzcon(.))’ needing to extend buffer size have failed (with HTTP/2 servers), reported by Gábor Csárdi.
‘predict(loess(..), se=TRUE)’ now errors out (instead of seg.faulting etc) for large sample sizes, thanks to a report and patch by Benjamin Tyner in PR#17121.
‘tools:assertCondition(., "error")’ and hence ‘assertError()’ no longer return errors twice (invisibly).
‘update(form, new)’ in the case of a long ‘new’ formula sometimes wrongly eliminated the intercept from ‘form’, or (more rarely) added a garbage term (or seg.faulted !); the fix happened by simplifying the C-level logic of ‘terms.formula()’. Reported by Mathias Ambühl in PR#16326.
The error message from ‘stopifnot(.., <error producing call>)’ again contains the full ‘"stopifnot(.......)"’ call: Its attempted suppression did not work consistently.
On Windows, ‘download.file(., , "wininet", headers=character())’ would fail; reported with patch proposal by Kevin Ushey in PR#17710.
R now provides a syntax for specifying raw character constants similar to the one used in C++: ‘r"(...)"’ with ‘...’ any character sequence, except that it must not contain the closing sequence ‘)"’. This makes it easier to write strings that contain backslashes or both single and double quotes. For more details see ‘?Quotes’.
‘norm(diag(c(1, NA)), "2")’ now works.
R now provides a syntax for specifying raw character constants similar to the one used in C++: ‘r"(...)"’ with ‘...’ any character sequence, except that it must not contain the closing sequence ‘)"’. This makes in easier to write strings that contain backslashes or both single and double quotes. For more details see ‘?Quotes’.
‘mle()’ in the ‘stats4’ package has had its interface extended so that arguments to the negative log-likelihood function can be one or more vectors, with similar conventions applying to bounds, start values, and parameter values to be kept fixed. NB: This has required a minor extension to class ‘"mle"’, so saved objects from earlier versions may need to be recomputed.
The ‘methods’ package does a better job of tracking inheritance relationships across packages.
New function ‘proportions()’ and ‘marginSums()’. These should replace the unfortunately named ‘prop.table()’ and ‘margin.table()’. They are drop-in replacements, but also add named-margin functionality. The old names are retained as aliases for back-compatibility.
On Windows, ‘download.file(., , "wininet", headers=character())’ would fail; reported with patch proposal by Kevin Ushey in PR#17710.
The error message from ‘stopifnot(.., <error producing call>)’ again contains the full ‘"stopifnot(.......)"’ call: Its attempted suppression did not work consistently.
‘update(form, new)’ in the case of a long ‘new’ formula sometimes wrongly eliminated the intercept from ‘form’, or (more rarely) added a garbage term (or seg.faulted !); the fix happened by simplifying the C-level logic of ‘terms.formula()’. Reported by Mathias Ambühl in PR#16326.
‘matplot(x,y)’ (and hence ‘matlines()’ and ‘matpoints()’) now call the corresponding methods of ‘plot()’ and ‘lines()’, e.g, when ‘x’ is a ‘"Date"’ or ‘"POSIXct"’ object; prompted by Spencer Graves' suggestion.
‘stopifnot()’ now allows customizing error messages via argument names, thanks to a patch proposal by Neal Fultz in PR#17688.
‘unlink()’ gains a new argument ‘expand’ to disable wildcard and tilde expansion.
‘smoothEnds(x)’ now returns ‘integer’ type in _both_ cases when ‘x’ is ‘integer’, thanks to report and proposal by Bill Dunlap PR#17693.
‘matrix’ objects now also inherit from class ‘"array"’, namely, e.g., ‘class(diag(1))’ is ‘c("matrix", "array")’ which invalidates code assuming that ‘length(class(obj)) == 1’, an incorrect assumption that is less frequently fulfilled now.
S3 methods for ‘"array"’, i.e., ‘<someFun>.array()’, are now also dispatched for ‘matrix’ objects.
R now builds by default against a PCRE2 library for Perl-like regular expressions if available at build time on non-Windows platforms (otherwise PCRE1 is used as in older versions of R).
PCRE2 is stricter in some cases and reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used, and reported as ‘FALSE’.
The version of PCRE used can be obtained via ‘extSoftVersion()’, PCRE1 has versions < 10, PCRE2 versions >= 10.
Operator ‘?’ now has lower precedence than ‘=’ to work as documented and to behave like ‘<-’ in help expressions (PR#16710).
‘round()’ finally rounds _“to nearest”_ by _measuring_ and _“to even”_; thanks to a careful algorithm originally prompted by the report from Adam Wheeler and then others, in PR#17668.
‘round(x, dig)’ for _negative_ digits is much more rational now, notably for large |dig|.
‘predict(loess(..), se=TRUE)’ now errors out (instead of seg.faulting etc) for large sample sizes, thanks to a report and patch by Benjamin Tyner in PR#17121.
‘tools:assertCondition(., "error")’ and hence ‘assertError()’ no longer return errors twice (invisibly).
For now only active when environment variable ‘_R_CLASS_MATRIX_ARRAY_’
is set to something true (i.e., one of ‘TRUE’, ‘True’, ‘true’, or ‘T’),
but planned to be the new unconditional behavior when R 4.0.0 is
released:
‘matrix’ objects now also inherit from class ‘"array"’, namely, e.g., ‘class(diag(1))’ is ‘c("matrix", "array")’ which invalidates code assuming that ‘length(class(obj)) == 1’, an incorrect assumption that is less frequently fulfilled now.
S3 methods for ‘"array"’, i.e., ‘<someFun>.array()’, are now also dispatched for ‘matrix’ objects.
R now builds by default against a PCRE2 library for Perl-like regular expressions if available at build time on non-Windows platforms (otherwise PCRE1 is used as in older versions of R).
PCRE2 is stricter in some cases and reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used, and reported as ‘FALSE’.
The version of PCRE used can be obtained via ‘extSoftVersion()’, PCRE1 has versions < 10, PCRE2 versions >= 10.
‘matrix’ objects now also inherit from class ‘"array"’, namely, e.g., ‘class(diag(1))’ is ‘c("matrix", "array")’ which invalidates code assuming that ‘length(class(obj)) == 1’, an incorrect assumption that is less frequently fulfilled now.
S3 methods for ‘"array"’, i.e., ‘<someFun>.array()’, are now also dispatched for ‘matrix’ objects.
‘sweep()’ and ‘slice.index()’ can now use names of dimnames for their ‘MARGIN’ argument (‘apply’ has had this for almost a decade).
New function ‘proportions()’ and ‘marginSums()’. The intention is that these should eventually replace the unfortunately named ‘prop.table()’ and ‘margin.table()’. They can be drop-in replacements, but also adds named-margin functionality.
‘sweep()’ and ‘slice.index()’ can now use names of dimnames for their ‘MARGIN’ argument (‘apply’ has had this for almost a decade). These functions, and also ‘asplit()’ have had the name of their first argument changed to ‘X’ for consistency with ‘apply()’
‘mle()’ in the ‘stats4’ package had problems combining use of box constraints and fixed starting values (in particular, confidence intervals were affected).
Uses of ‘url(gzcon(.))’ needing to extend buffer size have failed (with HTTP/2 servers), reported by Gábor Csárdi.
Functions ‘rbinom()’, ‘rgeom()’, ‘rhyper()’, ‘rpois()’, ‘rnbinom(),’ ‘rsignrank()’ and ‘rwilcox()’ which have returned integer since R 3.0.0 and hence ‘NA’ when the numbers would have been outside the integer range, now return double vectors (without NAs, typically) in these cases.
‘print()’'s default method and many other methods (by calling the default eventually and passing ‘...’) now make use of a new optional ‘width’ argument, avoiding the need for the user to set and reset ‘options("width")’.
‘sweep()’ can now use names of dimnames for its ‘MARGIN’ argument (‘apply’ has had this for almost a decade).
‘round()’ correctly rounds “to even” in more cases, thanks to a more careful algorithm prompted by the report from Adam Wheeler and then others, in PR#17668.
‘round(x, dig)’ for _negative_ digits is much more rational now, notably for large |dig|.
Fixed a C level integer overflow in ‘rhyper()’; reported by Benjamin Tyner in PR#17694.
‘sweep()’ can now use names of dimnames for its ‘MARGIN’ argument (apply has had this for almost a decade)
‘memDecompress()’ supports the RFC 1952 format (e.g. in-memory copies of ‘gzip’-compressed files) as well as RFC 1950.
‘memDecompress()’ supports the RFC 1652 format (e.g. in-memory copies of ‘gzip’-compressed files) as well as RFC 1650.
‘memCompress()’ and ‘memDecompress()’ support long raw vectors for types ‘"gzip"’ and ‘"zx"’.
‘print()’'s default method and many other methods (by calling the default eventually and passing ‘...’) now make use of a new optional ‘width’ argument, avoiding the need for the user to set and reset options("width").
‘mle()’ in the ‘stats’ package had problems combining use of box constraints and fixed starting values (in particular, confidence intervals were affected).
‘choose()’ misbehaved in corner cases where it switched ‘n - k’ for ‘k’ and ‘n’ was only _nearly_ integer (report from Erik Scott Wright).
‘print()’'s default method and many other methods (by calling the default eventually and passing ‘...’) now obey a new optional ‘width’ argument, the user not needing to set and unset the option.
‘head(x, n)’ and ‘tail()’ default and other S3 methods notably for _vector_ ‘n’, e.g. to get a “corner” of a matrix, also extended for ‘array’'s of higher dimension, thanks to the patch proposal by Gabe Becker in PR#17652. Consequently, optional argument ‘addrownums’ is deprecated and replaced by the (more general) ‘keepnums’. Invalid (2nd arg.) ‘n’ now leads to typically more easily readable error messages.
‘sequence()’ is now an S3 generic, with an internally implemented default method, and gains arguments to generate more complex sequences. Based on code from the ‘S4Vectors’ Bioconductor package and the advice of Hervé Pagès.
‘round()’ correctly rounds “to even” in more cases, thanks to a more careful algorithm prompted by the report from Adam Wheeler in PR#17668. (The current algorithm will be tweaked further before release.)
‘round(x, dig)’ for _negative_ digits is much more rational now, notably for large |dig|.
The warning message when attempting to export an nonexistent class is now more readable; thanks to Thierry Onkelinx for recognizing the problem.
‘sequence()’ is now an S3 generic, with an internally implemented default method, and gains arguments to generate more complex sequences. Based on code from the S4Vectors Bioconductor package and the advice of Hervé Pagès.
‘Rterm’ now accepts ALT+xxx sequences also with NumLock on. Tilde can be pasted with Italian keyboard (PR#17679).
‘sequence()’ is now a primitive and gains arguments to generate more complex sequences. Based on code from the S4Vectors Bioconductor package and the advice of Hervé Pagès.
Inheritance information on S4 classes is maintained more consistently, particularly in the case of class unions (in part due to PR#17596 and a report from Ezra Tucker).
‘is()’ behaves more robustly when ‘class2’ is a ‘classRepresentation’ object.
The warning message when attempting to export an nonexistant class is now more readable; thanks to Thierry Onkelinx for recognizing the problem.
‘update(form, new)’ in the case of a long ‘new’ formula sometimes wrongly eliminated the intercept from ‘form’, or (more rarely) added a garbage term (or seg.faulted !); reported by Mathias Ambühl in PR#16326.
‘round()’ correctly rounds “to even” in more cases, thanks to increased internal accuracy via code simplification proposed by Adam Wheeler in his report (PR#17668).
‘readBin()’ and ‘writeBin()’ now report an error for invalid ‘endian’ value. The affected code needs to be fixed with care as the old undocumented behavior was to swap endian-ness in such cases.
‘dnorm’ had a problematic corner case with ‘sd == -Inf’ and negative ‘sd’ was not flagged as error in all cases. Thanks to Stephen D. Weigand for reporting and Wang Jiefei for analyzing this; similar change in ‘dlnorm()’.
The optional ‘iter.smooth’ argument of ‘plot.lm()’, i.e., the ‘plot()’ method for ‘lm’ and ‘glm’ fits, now defaults to ‘0’ for all glm. Especially for binary observations with high or low fitted probabilities, this effectively deleted all observations of 1 or 0, respectively. Also, the type of residuals used in the ‘glm’ case has been switched to ‘"pearson"’ since deviance residuals do not in general have approximately zero mean.
In ‘plot.lm’, Cook's distance was computed from unweighted residuals, leading to inconsistencies. Replaced with usual weighted version. (PR#16056)
‘mcmapply’ in case of errors now preserves attributes of returned ‘"try-error"’ objects and avoids simplification, overriding ‘SIMPLIFY’ to ‘FALSE’. (PR#17653)
‘as.difftime()’ gets new optional ‘tz = "UTC"’ argument which should fix behaviour during daylight savings changeover days, fixing PR#16764, thanks to proposals and analysis by Johannes Ranke and Kirill Müller.
‘dnorm’ had a problematic corner case with ‘sd == -Inf’ and negative
‘sd’ was not flagged as error in all cases. Thanks to Stephen D.
Weigand for reporting and Wang Jiefei for analyzing this; similar
change in ‘dlnorm()’.
The ‘plot()’ method for ‘lm’ and ‘glm’ fits, ‘plot.lm()’, gains a new
option ‘iter.smooth’ with a default of ‘0’ for glm fits, no longer
down-weighting "outliers" when smoothing the residuals. Especially for
binary observations with high or low fitted probabilities, this
effectively deleted all observations of 1 or 0, respectively. Also, the
type of residuals used in the ‘glm’ case has been switched to
‘"pearson"’ since deviance residuals do not in general have
approximately zero mean.
In ‘plot.lm’, Cook's distance was computed from unweighted residuals,
leading to inconsistencies. Replaced with usual weighted version.
(PR#16056)
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.
New function ‘deparse1()’ produces one string, wrapping ‘deparse()’, to be used typically in ‘deparse1(substitute(*))’, e.g., to fix PR#17671.
‘wilcox.test()’ enhancements: In the (non-paired) two-sample case, ‘Inf’ values are treated as very large for robustness consistency. If exact computations are used, the result now has ‘"exact"’ in its ‘method’. New arguments ‘tol.root’ and ‘digits.rank’. The latter may be used for stability to treat very close numbers as ties.
Time-series ‘ts(*, start, end, frequency)’ with fractional ‘frequency’ are supported more consistently; thanks to a report from Johann Kleinbub and analysis and patch by Duncan Murdoch in PR#17669.
The included LAPACK has been updated to version 3.9.0 (for the included routines, just bug fixes).
‘dnorm’ had a problematic corner case with ‘sd == -Inf’ and negative ‘sd’ was not flagged as error in all cases. Thanks to Stephen D. Weigand for reporting and Wang Jiefei for analyzing this; similar change in ‘dlnorm()’.
‘dnorm’ had a problematic corner case with ‘sd == -Inf’ and negative ‘sd’ was not flagged as error in all cases. Thanks to Stephen D. Weigand for reporting and Wang Jiefei for analyzing this.
For now only active when environment variable ‘_R_CLASS_MATRIX_ARRAY_’ is set to something true (i.e., one of ‘TRUE’, ‘True’, ‘true’, or ‘T’), but planned to be the new unconditional behavior when R 4.0.0 is released:
‘matrix’ objects now also inherit from class ‘"array"’, namely, e.g., ‘class(diag(1))’ is ‘c("matrix", "array")’ which invalidates code assuming that ‘length(class(obj)) == 1’, an incorrect assumption that is less frequently fulfilled now.
S3 methods for ‘"array"’, i.e., ‘<someFun>.array()’, are now also dispatched for ‘matrix’ objects.
Where long vectors are available (i.e., almost everywhere), ‘writeBin()’ now allows long vectors, i.e., of length >= 2^31.
In ‘plot.lm’, Cook's distance was computed from unweighted residuals, leading to inconsistencies. Replaced with usual weighted version. (PR#16056)
‘sort.list(x)’ now works for non-atomic objects ‘x’ and ‘method="auto"’ (default) or ‘"radix"’ in cases ‘order(x)’ works.
New function ‘.class2()’ provides the full character vector of class names used for S3 method dispatch.
‘cm.colors(n)’ etc no longer append the code for ‘alpha = 1’, ‘"FF"’, to all colors. Hence all eight ‘*.colors()’ functions and ‘rainbow()’ behave consistently and have the same non-explicit default (PR#17659).
‘readBin()’ and ‘writeBin()’ of a ‘rawConnection()’ now also work in large cases, thanks to a report and proposal by Taeke Harkema in PR#17665.
The ‘plot()’ method for ‘lm’ and ‘glm’ fits, ‘plot.lm()’, gains a new option ‘iter.smooth’ with a default of ‘0’ for glm fits, no longer down-weighting "outliers" when smoothing the residuals. Especially for binary observations with high or low fitted probabilities, this effectively deleted all observations of 1 or 0, respectively. Also, the type of residuals used in the ‘glm’ case has been switched to ‘"pearson"’ since deviance residuals do not in general have approximately zero mean.
‘Rterm’ now works also when invoked from MSYS2 terminals. Line editing is possible when command ‘winpty’ is installed.
‘normalizePath()’ now resolves symbolic links and normalizes case of long names of path elements in case-insensitive folders (PR#17165).
‘md5sum()’ supports UTF-8 file names with characters that cannot be translated to the native encoding (PR#17633).
‘Rterm’ gains a new option ‘--workspace’ to specify the workspace to be restored. This allows equals to be part of the name when opening via Windows file associations (reported by Christian Asseburg).
R now uses reference counting instead of the ‘NAMED’ mechanism for determining when objects can be safely mutated in base C code. This reduces the need for copying is some cases and should allow further optimizations in the future. It should also help make the internal code easier to maintain. This change is expected to have minimal impact on packages not using unsupported coding practices in their C/C++ code.
(Windows) ‘Rterm’ now works also when invoked from MSYS2 terminals.
Line editing is possible when ‘winpty’ is installed.
‘normalizePath()’ on Windows now resolves symbolic links and normalizes
case of long names of path elements in case-insensitive folders
(PR#17165).
‘md5sum()’ on Windows supports UTF-8 file names with characters that
cannot be translated to the native encoding (PR#17633).
(Windows) ‘Rterm’ gains new option ‘--workspace’ to specify the
workspace to be restored. This allows equals to be part of the name
when opening via Windows file associations (reported by Christian
Asseburg).
Printing ‘methods(..)’ now uses new ‘format()’ method.
R now uses reference counting instead of the ‘NAMED’ mechanism for determining when objects can be safely mutated in base C code. This reduces the need for copying is some cases and should allow further optimizations in the future. It should also help make the internal code easier to maintain. This change is expected to have minimal impact on packages not using unsupported coding practices in their C code.
New function ‘.class2()’ provides the full character vector of class names used for S3 or S4 method dispatch.
‘conformMethod()’ now works correctly in cases containing a “‘&&’ logic” bug, reported by Henrik Bengtsson. It now creates methods with ‘"missing"’ entries in the signature. Consequently, ‘rematchDefinition()’ is amended to use appropriate ‘.local()’ calls with named arguments where needed.
‘conformMethod()’ now works correctly in cases containing a “‘&&’
logic” bug, reported by Henrik Bengtsson. It now creates methods with
‘"missing"’ entries in the signature. Consequently,
‘rematchDefinition()’ is amended to use appropriate ‘.local()’ calls
with named arguments where needed.
‘runmed(x, *)’ gains a new option ‘na.action’ determining _how_ to handle ‘NaN’ or ‘NA’ in ‘x’.
‘dotchart()’ gains new options ‘ann’, ‘xaxt’, ‘frame.plot’ and ‘log’.
Detection of the C stack direction has been moved from run-time to ‘configure’: this is safer with LTO builds and allows the detection to be overridden - see file ‘config.site’.
Source-code changes enable installation on platforms using ‘gcc -fno-common’ (the expected default for ‘gcc 10.x’).
‘installTrChar’ (which is nowadays is wrapped by ‘installChar’) is defined in ‘Rinternals.h’. (Neither are part of the API.)
Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at installation which is used by the prototypes in headers ‘R_ext/BLAS.h’ and ‘R_ext/Lapack.h’ but to avoid extensive breakage this is only exposed when ‘USE_FC_LEN_T’ is defined.
If a package's C/C++ calls to BLAS/LAPACK allow for the ‘hidden’ arguments used by most Fortran compilers to pass the lengths of Fortran character arguments, define ‘USE_FC_LEN_T’ and include ‘Rconfig.h’ (possibly _via_ ‘R.h’) before including ‘R_ext/BLAS.h’ or ‘R_ext/Lapack.h’.
A package with Fortran source code and perhaps C (but not C++) sources can request for its shared object/DLL to be linked by the Fortran compiler by including a line ‘USE_FC_TO_LINK=’ in ‘src/Makevars[.win]’ and using ‘$(SHLIB_OPENMP_FFLAGS)’ as part of ‘PKG_LIBS’.
The known reason for doing so is a package which uses Fortran (only) OpenMP on a platform where the Fortran OpenMP runtime is incompatible with the C one (e.g. ‘gfortran’ 9.x with ‘clang’).
‘R CMD check’ has a new option to mitigate checks leaving files/directories in ‘/tmp’. See the ‘R Internals’ manual - this is part of ‘--as-cran’.
The default standard for C++ in package installation is C++11 (as it has been on other platforms where available since R 3.6.0: the default toolchain on Windows was defaulting to C++98).
Support for specifying C++98 in package installation is deprecated.
Support in ‘R CMD config’ for ‘F77’, ‘FCPIFCPLAGS’, ‘CPP’, ‘CXXCPP’ and ‘CXX98’ and similar is deprecated. (‘CPP’ is found from the system ‘make’ and may well not be set.)
Use ‘$CC -E’ and ‘$CXX -E’ instead of ‘CPP’ and ‘CXXCPP’.
‘runmed(x, *)’ when ‘x’ contains missing values now works consistently for both ‘algorithm="Stuetzle"’ and ‘"Turlach"’, and no longer segfaults for ‘"Turlach"’, as reported by Hilmar Berger.
‘conformMethod()’ now works correctly in cases containing a “‘&&’ logic” bug, reported by Henrik Bengtsson. It now creates methods with ‘"missing"’ entries in the signature. Consequently, ‘rematchDefinition()’ is amended to use appropriate ‘.local()’ calls with named arguments where needed.
‘apply(diag(3), 2:3, mean)’ now gives a helpful error message.
‘dgamma(x, shape, log=TRUE)’ now longer overflows to ‘Inf’ for shape < 1 and very small ‘x’, fixing PR#17577, reported by Jonathan Rougier.
Buffer overflow in building error messages fixed. Reported by Benjamin Tremblay.
‘options(str = .)’ is correctly initialized at package ‘utils’ load time, now. A consequence is that ‘str()’ in scripts now is more consistent to interactive use, e.g., when displaying function(**) argument lists.
‘as.numeric(<call>)’ now gives correct error message.
Printing ‘ls.str()’ no longer wrongly shows ‘"<missing>"’ in rare cases.
Auto-printing S4 objects no longer duplicates the object, for faster speed and reduced memory consumption. Reported by Aaron Lun.
‘pchisq(<LRG>, <LRG>, ncp=100)’ no longer takes practically forever in some cases. Hence ditto for corresponding ‘qchisq()’ calls.
‘x %% L’ for finite ‘x’ no longer returns ‘NaN’ when ‘L’ is infinite, nor suffers from cancellation for large finite ‘L’, thanks to Long Qu's PR#17611.
Analogously, ‘x %/% L’ and ‘L %/% x’ suffer less from cancellation and return values corresponding to limits for large ‘L’.
‘grepl(NA, *)’ now returns ‘logical’ as documented.
‘options(warn=1e11)’ is an error now, instead of later leading to C stack overflow because of infinite recursion.
‘R_tryCatch’ no longer transfers control for all conditions. Reported and patch provided by Lionel Henry in PR#17617.
‘format(object.size(.), digits=NULL)’ now works, fixing PR#17628 reported by Jonathan Carroll.
‘get_all_vars(f, d)’ now also works for cases, e.g. where ‘d’ contains a matrix. Reported by Simon Wood in 2009 and patch provided by Ben Bolker in PR#13624.
Additionally, it now also works when some variables are data frames, fixing PR#14905, reported by Patrick Breheny.
‘barplot()’ could get spacings wrong if there were exactly two bars PR#15522. Patch by Michael Chirico.
‘power.t.test()’ works in more cases when returning values of n smaller than 2.
‘dotchart(*, pch=., groups=.)’ now works better. Reported by Robert and confirmed by Nic Rochette in PR#16953.
‘canCoerce(obj, cl)’ no longer assumes ‘length(class(obj)) == 1’.
‘plot.formula(*, subset = *)’ now also works in a boundary case reported by Robert Schlicht (TU Dresden).
For now only active when environment variable ‘_R_CLASS_MATRIX_ARRAY_’ is set to non-empty, but planned to be the new unconditional behavior when R 4.0.0 is released:
‘matrix’ objects now also inherit from class ‘"array"’, namely, e.g., ‘class(diag(1))’ is ‘c("matrix", "array")’ which invalidates code assuming that ‘length(class(obj)) == 1’, an incorrect assumption that is less frequently fulfilled now.
S3 methods for ‘"array"’, i.e., ‘<someFun>.array()’, are now also dispatched for ‘matrix’ objects.
Better error message for ‘contour(*, levels = Inf)’.
The Fortran code for calculating the ‘coefficients’ component in ‘lm.influence’ was very inefficient. It has (for now) been replaced with much faster R code (PR#17624).
‘cm.colors(n)’ etc no longer append the code for ‘alpha = 1’, ‘"FF"’, to all colors. Hence all eight ‘*.colors()’ functions and ‘rainbow()’ behave consistently (PR#17659).
‘runmed(x, *)’ gains a new option ‘na.action’ determining _how_ to handle ‘NaN’ or ‘NA’ in ‘x’.
‘dotchart()’ gains new options ‘ann’, ‘xaxt’, ‘frame.plot’ and ‘log’.
Source-code changes enable installation on platforms using ‘gcc -fno-common’ (the expected default for ‘gcc 10.x’).
The default standard for C++ in package installation is C++11 (as it has been on other platforms where available since R 3.6.0: the default toolchain on Windows was defaulting to C++98).
‘plot.formula(*, subset = *)’ now also works in a boundary case reported by Robert Schlicht (TU Dresden).
‘head(x, n)’ and ‘tail()’ default and other S3 methods notably for _vector_ ‘n’, e.g. to get a “corner” of a matrix, also extended for ‘array’'s of higher dimension, thanks to the patch proposal by Gabe Becker in PR#17652.
‘head(x, n)’ and ‘tail()’ default and other S3 methods notably for _vector_ ‘n’, e.g. to get a “corner” of a matrix, also extended for ‘array’'s of higher dimension, thanks to the patch proposal by Gabe Becker in PR#16764.
‘cm.colors(n)’ etc no longer append ‘alpha=1’ codes ‘"FF"’ to all colors. Hence all eight ‘*.colors()’ functions and ‘rainbow()’ behave consistently, PR#17659.
‘n2mfrow()’ gains an option ‘asp = 1’ to specify the aspect ratio, fulfilling the wish and extending the proposal of Michael Chirico in PR#17648.
For now only active when environment variable ‘_R_CLASS_MATRIX_ARRAY_’ is set to non-empty, but planned to be the new unconditional behavior when R 4.0.0 is released:
Newly, ‘matrix’ objects also inherit from class ‘"array"’, namely, e.g., ‘class(diag(1))’ is ‘c("matrix", "array")’ which invalidates code (wrongly) assuming that ‘length(class(obj)) == 1’, a wrong assumption that is less frequently fulfilled now. (Currently only after setting ‘_R_CLASS_MATRIX_ARRAY_’ to non-empty.)
S3 methods for ‘"array"’, i.e., ‘<someFun>.array()’, are now also dispatched for ‘matrix’ objects.
For now only active when environment variable ‘_R_CLASS_MATRIX_ARRAY_’ is set to non-empty, but planned to be the new unconditional behavior when R 4.0.0 is released:
Newly, ‘matrix’ objects also inherit from class ‘"array"’, namely, e.g., ‘class(diag(1))’ is ‘c("matrix", "array")’ which invalidates code (wrongly) assuming that ‘length(class(obj)) == 1’, a wrong assumption that is less frequently fulfilled now (currently only after setting ‘_R_CLASS_MATRIX_ARRAY_’ to non-empty).
The Fortran code for calculating the ‘coefficients’ component in ‘lm.influence’ was very inefficient. It has (for now) been replaced with much faster R code. PR#17624
‘get_all_vars(f, d)’ now also works for cases, e.g. where ‘d’ contains a matrix. Reported by Simon Wood in 2009 and patch provided by Ben Bolker in PR#13624.
Additionally, it now also works when some variables are data frames, fixing PR#14905, reported by Patrick Breheny.
The default standard for C++ in package installation is C++11 (as it has been on other platforms if available since R 3.6.0: the default toolchain on Windows was defaulting to C++98).
(Windows) ‘Rterm’ now correctly displays multi-byte coded characters representable in the current native encoding (at least on Windows 10 they were sometimes omitted, PR#17632).
‘canCoerce(obj, cl)’ no longer assumes ‘length(class(obj)) == 1’.
(Windows) ‘Rterm’ gains new option ‘--workspace’ to specify the workspace to be restored. This allows equals to be part of the name when opening via Windows file associations (reported by Christian Asseburg).
Primitive replacement functions no longer mutate a referenced first argument when used outside of a complex assignment context.
‘md5sum()’ on Windows supports UTF-8 file names with characters that cannot be translated to the native encoding (PR#17633).
Better error message for ‘contour(*, levels=Inf)’.
‘contourLines()’' value is no longer ‘invisible()’.
‘Sys.glob()’ on Windows now supports all characters from the BMP, no longer corrupting (less commonly used) characters (PR#17638).
Primitive replacement functions no longer mutate a referenced first argument when used outsinde of a complex assignment context.
A package with Fortran source code and perhaps C (but not C++) sources can request for its shared object/DLL to be linked by the Fortran compiler by including a line ‘USE_FC_TO_LINK=’ in ‘src/Makevars[.win]’ and using ‘$(SHLIB_OPENMP_FFLAGS)’ as part of ‘PKG_LIBS’.
The known reason for doing so is a package which uses Fortran (only) OpenMP on a platform where the Fortran OpenMP runtime is incompatible with the C one (e.g. ‘gfortran’ 9.x with ‘clang’).
The ‘palette()’ function has a new default set of colours (which are less saturated and have better accessibility properties). There are also some new built-in palettes, which are listed by the new ‘palette.pals()’ function. These include the old default palette under the name ‘"R3"’. Finally, the new ‘palette.colors()’ function allows a subset of colours to be selected from any of the built-in palettes.
‘write.dcf()’ no longer mangles field names (PR#17589).
‘normalizePath()’ on Windows now resolves symbolic links and normalizes case of long names of path elements in case-insensitive folders (PR#17165).
‘x %% L’ for finite ‘x’ no longer returns ‘NaN’ when ‘L’ is infinite,
nor suffers from cancellation for large finite ‘L’, thanks to Long Qu's
PR#17611.
Analogously, ‘x %/% L’ and ‘L %/% x’ suffer less from cancellation and return values corresponding to limits for large ‘L’.
‘dotchart()’ gets new options ‘ann’, ‘xaxt’, ‘frame.plot’ and ‘log’.
‘x %% L’ for finite ‘x’ no longer returns ‘NaN’ when ‘L’ is infinite, nor suffers from cancellation for large finite ‘L’, thanks to Long Qu's PR#17611.
Analogously, ‘x %/% L’ and ‘L %/% x’ suffer less from cancellation and return values corresponding to limits for large ‘L’.
‘dotchart(*, pch=., groups=.)’ now works better. Reported by Robert and confirmed by Nic Rochette in PR#16953.
‘R CMD check’ now optionally checks ‘configure’ and ‘cleanup’ scripts for non-Bourne-shell code (‘bashisms’).
‘power.t.test()’ works in more cases when returning values of n smaller than 2.
‘barplot()’ could get spacings wrong if there were exactly two bars PR#15522. Patch by Michael Chirico.
The formula interface to ‘t.test()’ and ‘wilcox.test()’ has been extended to handle one-sample and paired tests.
‘barplot()’ could get spacings wrong if there was exactly two bars PR#15522. Patch by Michael Chirico.
‘get_all_vars(f, d)’ now also works for cases, e.g. where ‘d’ contains a matrix. Reported by Simon Wood in 2009 and patch provided by Ben Bolker in PR#13624.
The formula interface to ‘t.test’ and ‘wilcox.test’ has been extended to handle one-sample and paired tests.
The internal traceback object produced when an error is signalled (‘.Traceback’), now contains the ‘call’s rather than the _‘deparse()’d_ calls, deferring the deparsing to the user-level functions ‘.traceback()’ and ‘traceback()’, fulfilling the wish of PR#17580, reported incl. two patch proposals by Brodie Gaslam.
‘methods(class = class(glm(..)))’ now warns more usefully and only once.
‘format(object.size(.), digits=NULL)’ now works, fixing PR#17628 reported by Jonathan Carroll.
‘R_tryCatch’ no longer transfers control for all conditions. Reported and patch provided by Lionel Henry in PR#17617.
The backquote function ‘bquote()’ has a new argument ‘splice’ to enable splicing a computed list of values into an expression, like ‘,@’ in LISP's backquote.
The formula interface to ‘t.test’ has been extended to handle one-sample and paired tests.
‘R_tryCatch’ no longer transfers control for all conditions. Reported and patch provided by Linoel Henry in PR#17617.
The internal version number of R-devel has been set to 4.0.0, reflecting the intention that the next non-patch release should be 4.0.0.
‘R --help’ now mentions the option ‘--no-echo’ (renamed from ‘--slave’) and its previously undocumented short form ‘-s’.
‘options(warn=1e11)’ is an error now, instead of later leading to C stack overflow because of infinite recursion.
‘grepl(NA, *)’ now returns ‘logical’ as documented.