This blog is updated daily.
A general description is here.
‘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.
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.
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 deprecated support for specifying C++98 in package installation has been removed.
Certain ‘Ops’ (notably comparison such as ‘==’) now also work for 0-length data frames, after reports by Hilmar Berger.
‘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’.
R now builds by default against 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.
Either PCRE >= 8.32 (Nov 2012) or PCRE2 is required: the deprecated provision for 8.20-8.31 has been removed.
The minimum required version of ‘libcurl’ is now 7.28.0 (Oct 2012).
PCRE2 is used if available: this is strongly recommended as PCRE1 is no longer developed (it only receives bug fixes and has outdated Unicode tables). ‘configure’ will warn if PCRE2 is not found and fall back to PCRE1. ‘configure’ options ‘--without-pcre1’ and ‘--without-pcre2’ can be used to exclude one or the other (but at least one of PCRE2 and PCRE1 is required).
R now builds by default against 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.
Add 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.
PCRE2 is used if available: this is strongly recommended as PCRE1 is no longer developed (it only receives bug fixes and has outdated Unicode tables).
‘postscript(.., title = *)’ now signals an error when the title string contains a character which produces corrupt PostScript, thanks to Daisuko Ogawa's PR#17607.
Most functions with file-path inputs will give an explicit error if a file-path input in a marked encoding cannot be translated (to the native encoding or in some cases on Windows to UTF-8), rather than translate to a different file path using escapes. Some (such as ‘dir.exists()’, ‘file.exists()’, ‘file.access()’, ‘file.info()’, ‘list.files()’, ‘normalizePath()’ and ‘path.expand()’) treat this like any other non-existent file, often with a warning.
There is a new function ‘infoRDS()’ providing information about the serialization format of a serialized object.
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]’.
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’).
Add an arguemnt ‘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.
Header ‘R_ext/Print.h’ defines ‘R_USE_C99_IN_CXX’ and hence exposes ‘Rvprintf’ and ‘REprintf’ if used with a C++11 compiler.
allow ‘add_datalist(*, small.size=0)’ to create a ‘data/datalist’ file
also in case the data sets are small.
S3 method lookup now by default skips the elements of the search path between the global and base environments.
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’.
‘pchisq(<LRG>, <LRG>, ncp=100)’ no longer takes practically forever in some cases. Hence ditto for corresponding ‘qchisq()’ calls.
Support for specifying C++98 in package installation has been removed.
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.)
Support in ‘R CMD config’ for ‘F77’, ‘FCPIFCPLAGS’, ‘CXXCPP’ and ‘CXX98’ and similar is deprecated.
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’.
‘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’.
‘format(as.symbol("foo"))’ now works (returning ‘"foo"’).
allow ‘add_datalist(*, small.size=0)’ to create a ‘data/datalist’ file also in case the data sets are small.
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 serialization format of a serialized object.
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.
(Windows) ‘Rterm’ now works also when invoked from MSYS2 terminals. Line editing is possible when ‘winpty’ is installed.
‘iconv()’ has a new option ‘sub = "Unicode"’ to translate UTF-8 input invalid in the ‘to’ encoding using ‘<U+xxxx>’ escapes.
New function ‘list2DF()’ for creating data frames from lists of variables.
‘R CMD config’ no longer knows about the unused settings ‘F77’ and ‘FCPIFCPLAGS’, nor ‘CXX98’ and similar.
Support for specifying C++98 in package installation is deprecated.
‘installTrChar’ (which is nowadays is wrapped by ‘installChar’) is defined in ‘Rinternals.h’. (Neither are part of the API.)
‘Rterm’ now works also when invoked from MSYS2 terminals. Line editing is possible when ‘winpty’ is installed.
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()’, ‘normalizePath()’ and ‘path.expand()’) treat this like any other non-existent file, with a warning.
‘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 using escapes as previously.
A C++ compiler default is set only if the C++11 standard is supported: it no longer falls back to C++98.
‘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’.
‘installTrChar’ which is nowadays a wrapper for ‘installChar’ is defined in ‘Rinternals.h’. (Neither are part of the API.)
‘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.
Most functions with file-path inputs will give an explicit error if a file-path input in a marked encoding cannot be translated (to UTF-8 or the native encoding), rather than translate using escapes as previously.
‘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).
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. patch proposal) by Brodie Gaslam.
‘package.skeleton()’ now explicitly lists all exports in the ‘NAMESPACE’ file.
‘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 UTF-8 and marked as such.
‘package.skeleton()’ now explicitly lists all exports.
New function ‘.S3method()’ to register S3 methods in R scripts.
‘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.
‘data.matrix()’ now converts character columns to factors and from this to integers.
‘format.default(*, scientific = FALSE)’ now corresponds to a practically most extreme ‘options(scipen = n)’ setting rather than arbitrary ‘n = 100’.
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. patch proposal) by Brodie Gaslam.
Auto-printing S4 objects no longer duplicates the object, for faster speed and reduced memory consumption. Reported by Aaron Lun.
‘as.numeric(<call>)’ now gives correct error message.
Printing ‘ls.str()’ no longer wrongly shows ‘"<missing>"’ in rare cases.
‘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 whish of PR#17580, reported (incl. patch proposal) by Brodie Gaslam.
‘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.
‘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.
Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at
installation which is used by the prototypes in headers ‘BLAS.h’ and
‘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 use 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 ‘BLAS.h’ or ‘Lapack.h’.
Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at installation which is used by the prototypes in headers ‘BLAS.h’ and ‘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 ‘BLAS.h’ or ‘Lapack.h’.
‘apply(diag(3), 2:3, mean)’ now gives a helpful error message.
‘conformMethod()’ also gives correct error messages in another case of
signature mismatches, reported by Suharto Anggono.
‘conformMethod()’ also gives correct error messages in another case of signature mismatches, reported by Suharto Anggono.
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’.
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’.
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.
‘runmed(x, *)’ gets new option ‘na.action’ determining _how_ to handle ‘NaN’ or ‘NA’ in ‘x’.
‘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 correctly works 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, *)’ gets new option ‘na.action’ determining how to handle
‘NaN’ or ‘NA’ in ‘x’.
‘runmed(x, *)’ when ‘x’ contains missing values now works consistently
for both ‘algorithm="Stuetzle"’ and ‘"Turlach"’, also based on
‘smoothEnds(y)’ working with ‘NA’s, and no longer segfaults for
‘"Turlach"’, as reported by Hilmar Berger.
Improvements in ‘smoothEnds(x, *)’ working with ‘NA’s (towards ‘runmed()’ working in that case, in the next version of R).
‘runmed(x, *)’ gets new option ‘na.action’ determining how to handle ‘NaN’ or ‘NA’ in ‘x’.
‘runmed(x, *)’ when ‘x’ contains missing values now works consistently for both ‘algorithm="Stuetzle"’ and ‘"Turlach"’, also based on ‘smoothEnds(y)’ working with ‘NA’s, and no longer segfaults for ‘"Turlach"’, as reported by Hilmar Berger.
‘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.
‘methods:::conformMethod()’ had ‘&&’ where ‘&’ was needed. (Spotted by
Henrik Bengtsson.)
‘methods:::conformMethod()’ had ‘&&’ where ‘&’ was needed. (Spotted by Henrik Bengtsson.)
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.
‘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 Windows, ‘writeClipboard(.., format = <n>)’ now does correctly pass ‘format’ to the underlying C code, thanks to a bug report (with patch) by Jenny Bryan.
‘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.
‘vcov(glm(<quasi>), dispersion = *)’ works correctly again, fixing PR#17571 thanks to Pavel Krivitsky.
‘runmed(x, *)’ when ‘x’ contains missing values now works for ‘algorithm="Stuetzle"’, also based on ‘smoothEnds(y)’ working with NA's, and no longer segfaults for the ‘"Turlach"’ algorithm; reported by Hilmar Berger.
Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at installation which is used by the prototypes in headers ‘BLAS.h’ and ‘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 use 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 ‘BLAS.h’ or ‘Lapack.h’.
‘R CMD config’ knows the values of ‘AR’ and ‘RANLIB’, often set for LTO builds.